Methods related to bronchial premalignant lesion severity and progression

ABSTRACT

The technology described herein is directed to methods of treating and diagnosing bronchial premalignant lesions, e.g. by determining the lesion subtype using one or more biomarkers described herein.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a divisional under 35 U.S.C. § 121 of co-pendingU.S. Ser. No. 16/545,032 filed Aug. 20, 2019, which claims benefit under35 U.S.C. § 119(e) of U.S. Provisional Application No. 62/765,264 filedAug. 20, 2018, the contents of which are incorporated herein byreference in their entireties.

GOVERNMENT SUPPORT

This invention was made with Government Support under Contract No.CA196408 awarded by the National Institutes of Health. The Governmenthas certain rights in the invention.

TECHNICAL FIELD

The technology described herein relates to treatment, diagnosis, andmonitoring of treatment for bronchial premalignant lesions.

BACKGROUND

Lung squamous cell cancer develops from non-cancerous lesions in theairway known as bronchial premalignant lesions. The presence ofpersistent or progressive dysplastic bronchial premalignant lesions is amarker of increased lung cancer risk both at the lesion site (where theyare the presumed precursors of squamous cell lung cancer) and elsewherein the lung. Not all bronchial premalignant lesions progress to invasivecancer, and those that do, progress at variable rates with variableoutcomes. At present, there are no tools available in the clinic toidentify which lesions will progress to cancer and which will not.Additionally, the current technology for detecting bronchialpremalignant lesions is via autofluorescence and white-lightbronchoscopy. A bronchoscopy procedure is invasive and is onlymoderately sensitive and specific at detecting small bronchialpremalignant lesions as it requires visualization of the lesions.Finally, to date, the only treatment for bronchial premalignant lesionsis to remove the lesions via surgery or bronchoscopy.

SUMMARY

The inventors have now developed: 1) tests for the presence of bronchialpremalignant lesions (some of which do not require bronchoscopy and usethe surprising finding that normal tissues elsewhere in the airwayexhibit biomarkers indicating the presence of bronchial premalignantlesions in the subject), 2) methods for determining if the bronchialpremalignant lesions is likely to progress to cancer, 3) new therapiesfor bronchial premalignant lesions which target the underlying molecularchanges which characterize the bronchial premalignant lesions.

Accordingly, provided herein one aspect is a method of treatingbronchial premalignant lesions, the method comprising: administering atleast one of: (i) both a bronchoscopy-based procedure to survey thecentral airway and a chest CT scan; (ii) at least every 6 months, one ofa bronchoscopy-based procedure to survey the central airway and a chestCT scan; and/or (iii) at least one anti-proliferative drug; to a subjectdetermined to have at least one of: (a) an increased level of expressionof at least one module 5 gene as compared to a non-proliferative lesionreference level; and (b) a decreased level of expression of at least onemodule 6 gene as compared to a non-proliferative lesion reference level.

In one embodiment of this aspect and all other aspects provided herein,the at least one module 5 gene is selected from the group consisting of:RACGAP1 and TPX2; and the at least one module 6 gene is selected fromthe group consisting of: NEK11 and IFT88.

In another embodiment of this aspect and all other aspects providedherein, the subject is further determined to have an increased level ofexpression of at least one module 7 or module 4 gene.

In another embodiment of this aspect and all other aspects providedherein, the at least one module 7 or module 4 gene is selected from thegroup consisting of: COX6A1; COX7A2; RPL26; and RPL23.

In another embodiment of this aspect and all other aspects providedherein, the level of expression of each of the genes of Table 15 isdetermined. The method of any of claims 1-5, wherein the at least oneanti-proliferative drug is selected from the group consisting of:Acetylcholine receptor antagonist; Acetylcholinesterase inhibitors;Adenosine receptor antagonists; Adrenergic receptor antagonists; AKTinhibitors; Angiotensin receptor antagonists; Apoptosis stimulants;Aurora kinase inhibitors; CDK inhibitors; Cyclooxygenase inhibitors;Cytokine production inhibitors; Dehydrogenase inhibitors; DNA proteinkinase inhibitors; focal adhesion inhibitors; Dopamine receptorantagonist; EGFR inhibitors; ERK1 and ERK2 phosphorylation inhibitors;Estrogen receptor agonists; EZH2 inhibitors; FLT3 inhibitors;Glucocorticoid receptor agonists; Glutamate receptor antagonists; HDACinhibitors; Histamine receptor antagonists; Histone lysinemethyltransferase inhibitors; HSP inhibitors; IKK inhibitors; Ionchannel antagonists; JAK inhibitors; JNK inhibitors; KIT inhibitors;Leucine rich repeat kinase inhibitors; MDM inhibitors; mediator releaseinhibitors; MEK inhibitors; MTOR inhibitors; Monoamine oxidaseinhibitors; NFkB pathway inhibitors; nucleophosmin inhibitors; PARPinhibitors; PPAR receptor agonists; PI3K inhibitors; tyrosine kinaseinhibitors; Phosphodiesterase inhibitors; protein kinase inhibitors; RAFinhibitors; RNA polymerase inhibitors; topoisomerase inhibitors; RNAsynthesis inhibitors; SIRT inhibitors; sodium channel blockers; VEGFRinhibitors; and Vitamin D receptor agonists.

In another embodiment of this aspect and all other aspects providedherein, the anti-proliferative drug is administered as an inhaledformulation or topical formulation.

In another embodiment of this aspect and all other aspects providedherein, the anti-proliferative drug is administered during abronchoscopy-based procedure.

In another embodiment of this aspect and all other aspects providedherein, the anti-proliferative drug is administered systemically.

In another embodiment of this aspect and all other aspects providedherein, the anti-proliferative drug is administered during abronchoscopy-based procedure and systemically.

Another aspect provided herein relates to a method of treating bronchialpremalignant lesions, the method comprising: administering at least oneof: (i) both a bronchoscopy-based procedure to survey the central airwayand a chest CT scan; (ii) at least every 6 months, one of abronchoscopy-based procedure to survey the central airway and a chest CTscan; and/or (iii) at least one anti-proliferative drug; to a subjectdetermined to have at least one of: (a) an increased level of expressionof at least one module 5 gene as compared to a non-proliferative lesionreference level; and (b) a decreased level of expression of at least onemodule 6 gene as compared to a non-proliferative lesion reference level,wherein the subject is further determined to have a decreased level ofexpression of at least one module 9 gene as compared to anon-proliferative lesion reference level and/or an increased level ofexpression of at least one module 10 gene as compared to anon-proliferative lesion reference level.

In one embodiment of this aspect and all other aspects provided herein,the subject determined to have a decreased level of expression of atleast one module 9 gene and/or an increased level of expression of atleast one module 10 gene is administered at least one of:

-   -   i. both a bronchoscopy-based procedure to survey the central        airway wherein the lesions are biopsied to remove abnormal        tissue and a chest CT scan;    -   ii. at least every 6 months, one of a bronchoscopy-based        procedure to survey the central airway wherein the lesions are        biopsied to remove abnormal tissue and a chest CT scan; and/or    -   iii. at least one immune stimulating drug.

Also provided herein, in another aspect, is a method of treatingbronchial premalignant lesions, the method comprising: administering atleast one of: (i) both a bronchoscopy-based procedure to survey thecentral airway wherein the lesions are biopsied to remove abnormaltissue and a chest CT scan; (ii) at least every 6 months, one of abronchoscopy-based procedure to survey the central airway wherein thelesions are biopsied to remove abnormal tissue and a chest CT scan;and/or (iii) at least one immune stimulating drug; to a subjectdetermined to have a decreased level of expression of at least onemodule 9 gene as compared to a non-proliferative lesion reference leveland/or an increased level of expression of at least one module 10 geneas compared to a non-proliferative lesion reference level.

In one embodiment of this aspect and all other aspects provided herein,the module 9 gene is selected from the group consisting of: EPSTI1;UBE2L6; B2M and TAP1.

In another embodiment of this aspect and all other aspects providedherein, the at least one gene module 9 gene is selected from Table 16.

In another embodiment of this aspect and all other aspects providedherein, the module 10 gene is selected from the group consisting of:CACNB3 and MAPK10.

In another embodiment of this aspect and all other aspects providedherein, the at least one immune stimulating drug is selected from thegroup consisting of: immune-checkpoint inhibitors (e.g. inhibitorsagainst, PD-1, PD-L1, CTLA4, and LAG3); drugs that stimulate interferonsignaling (e.g. anti-viral drugs that improve interferon signaling); DNAsynthesis inhibitors; IMDH inhibitors; CDK inhibitors; ribonucleotidereductase inhibitors; dihydrofolate reductase inhibitors; topoisomeraseinhibitors; FLT3 inhibitors; IGF-1 inhibitors; MEK inhibitors; aurorakinase inhibitors; PKC inhibitors; RAF inhibitors; PDFGR/KIT inhibitors;VEGFR inhibitors; SRC inhibitors; retinoid receptor agonists; HDACinhibitors; DNA methyltransferase inhibitors; and EZH2 inhibitors.

Another aspect provided herein relates to a method of treating bronchialpremalignant lesions, the method comprising: administering at least oneof: (i) both a bronchoscopy-based procedure to survey the central airwayand a chest CT scan; (ii) at least every 6 months, one of abronchoscopy-based procedure to survey the central airway and a chest CTscan; and/or (iii) at least one anti-inflammatory drug; to a subjectdetermined to have at least one of: (a) an increased level of expressionof at least one module 2 gene as compared to a non-inflammatoryreference level; and (b) a decreased level of expression of at least onemodule 6 gene as compared to a non-inflammatory reference level.

In one embodiment of this aspect and all other aspects provided herein,the at least one module 2 gene is selected from the group consisting of:MSANTD2, CCNL2, and LUC7L; and the at least one module 6 gene isselected from the group consisting of: NEK11 and IFT88.

In another embodiment of this aspect and all other aspects providedherein, the subject is further determined to have an increased level ofexpression of at least one module 7 gene, module 1 gene, or module 8gene and/or decreased level of expression of at least one module 4 geneor one module 5 gene.

In another embodiment of this aspect and all other aspects providedherein, the at least one module 7 gene is selected from the groupconsisting of: RPL26 and RPL23.

In another embodiment of this aspect and all other aspects providedherein, the at least one module 1 gene is selected from the groupconsisting of: KIRREL; PHLDB1; and MARVELD1.

In another embodiment of this aspect and all other aspects providedherein, the at least one module 8 gene is selected from the groupconsisting of: DOC2; CD53; and LAP™.

In another embodiment of this aspect and all other aspects providedherein, the at least one module 4 gene is selected from the groupconsisting of: COX6A1 and COX7A2

In another embodiment of this aspect and all other aspects providedherein, the at least one module 5 gene is selected from the groupconsisting of: RACGAP1 and TPX2

In another embodiment of this aspect and all other aspects providedherein, the level of expression of each of the genes of Table 15 isdetermined.

In another embodiment of this aspect and all other aspects providedherein, the at least one anti-inflammatory drug is selected from thegroup consisting of: Acetylcholine receptor antagonists;Acetylcholinesterase inhibitors; Adenosine receptor antagonists;Adrenergic receptor antagonists; Angiotensin receptor antagonists;Anti-IL1B antibodies; Apoptosis stimulants; Aurora kinase inhibitors;CDK inhibitors; Cyclooxygenase inhibitors; Cytokine productioninhibitors; Dehydrogenase inhibitors; Dopamine receptor antagonists;EGFR inhibitors; ERK1 and ERK2 phosphorylation inhibitors; Estrogenreceptor agonists; FLT3 inhibitors; Glucocorticoid receptor agonists;Glutamate receptor antagonists; HDAC inhibitors; Histamine receptorantagonists; Histone lysine methyltransferase inhibitors; HSPinhibitors; IKK inhibitors; Ion channel antagonists; KIT inhibitors;Leucine rich repeat kinase inhibitors; MEK inhibitors; MDM inhibitors;Phosphodiesterase inhibitors; Monoamine oxidase inhibitors; MTORinhibitors; NFkB pathway inhibitors; nucleophosmin inhibitors; PARPinhibitors; PI3K inhibitors; PPAR receptor agonists; protein synthesisinhibitors (e.g. chloramphenicol); RAF inhibitors; SIRT inhibitors;Sodium channel blockers; TGF beta receptor inhibitors; Topoisomeraseinhibitors; Tyrosine kinase inhibitors; VEGFR inhibitors; and Vitamin Dreceptor agonists.

In another embodiment of this aspect and all other aspects providedherein, the anti-inflammatory drug is administered during abronchoscopy-based procedure.

In another embodiment of this aspect and all other aspects providedherein, the anti-inflammatory drug is administered systemically.

In another embodiment of this aspect and all other aspects providedherein, the anti-inflammatory drug is administered during abronchoscopy-based procedure and systemically.

In another embodiment of this aspect and all other aspects providedherein, the at least one gene is selected from Table 14.

In another embodiment of this aspect and all other aspects providedherein, the level of expression of each of the genes of Table 14 isdetermined.

In another embodiment of this aspect and all other aspects providedherein, whereby the development of lung cancer lung squamous cellcarcinoma is prevented, delayed, or slowed.

In another embodiment of this aspect and all other aspects providedherein, wherein the lung cancer is lung squamous cell carcinoma.

In another embodiment of this aspect and all other aspects providedherein, the level of expression is the level of expression in anendobronchial biopsy, endobronchial brushing sample, large airwaybiopsy, large airway brushing sample, nasal epithelial cells, sputum, orblood obtained from the subject.

In another embodiment of this aspect and all other aspects providedherein, the level of expression is the level of expression in abronchial brushing obtained from the right or left mainstem bronchus.

In another embodiment of this aspect and all other aspects providedherein, the biopsy or brushing sample comprises morphologically-normaltissues or cells.

In another embodiment of this aspect and all other aspects providedherein, the biopsy or brushing sample consists of morphologically-normaltissues or cells.

In another embodiment of this aspect and all other aspects providedherein, the level of expression is the level of expression in a samplecomprising bronchial premalignant lesion cells.

In another embodiment of this aspect and all other aspects providedherein, the level of expression is the level of expression in a samplecomprising morphologically-normal cells.

In another embodiment of this aspect and all other aspects providedherein, the subject is a smoker or former smoker.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1E demonstrate that endobronchial biopsies divide into fourdistinct molecular subtypes that correlate with clinical and molecularphenotypes. (FIG. 1A) Genes (n=3,936) organized into 9 geneco-expression modules were used to discover four molecular subtypes(Proliferative, Inflammatory, Secretory, and Normal-like) across the 190DC biopsies using consensus clustering. The heatmap showssemi-supervised hierarchal clustering of z-score normalized geneexpression across the 3,936 genes and 190 DC biopsies. The top barrepresents the four molecular subtypes: Proliferative (n=52 samples),Inflammatory (n=37 samples), Secretory (n=61 samples), and Normal-like(n=40 samples). Throughout all figures, the four molecule subtypes arerepresented by four shades of grey, increasing in lightness respectiveto the order given in the previous sentence. On the left side of theheatmap, the mean of the first principal component calculated acrossmodule genes is plotted for each subtype. On the right side of theheatmap, a summary of enriched biological pathways is listed for eachmodule. (FIG. 1B) Bubbleplots showing significant associations (p<0.01by Fisher's Exact Test) between the molecular subtypes and smokingstatus, biopsy histological grade, and the predicted LUSC tumormolecular subtypes. The columns represent the 4 molecular subtypes(Proliferative, Inflammatory, Secretory, and Normal-like) and thediameter of the circle is proportional to the number of samples withineach subtype that have the row phenotype. (FIG. 1C) Boxplot ofexpression values of MKI67 in biopsies with normal or hyperplasiahistology (n=8, 16, 26, 18 in Proliferative, Inflammatory, Secretory,and Normal-like subtypes, respectively). The MKI67 expression levels ofthe Proliferative subtype are significantly greater thannon-Proliferative subtype samples (FDR=3.4e-10) (FIG. 1D) Boxplot ofexpression values of MKI67 in biopsies with dysplastic histology (n=33,11, 19, 9 in Proliferative, Inflammatory, Secretory, and Normalsubtypes, respectively). The MKI67 expression levels of theProliferative subtype are significantly greater than non-Proliferativesubtype samples (FDR=3.1e-8). (FIG. 1E) Immunofluorescent stainingdemonstrating the increased MKI67 and KRT5 staining and reduced TUB1A1staining in the Proliferative subtype in concordance with the expressionof the corresponding marker genes. The representative samples shown forthe Proliferative and Inflammatory subtypes have dysplasia histologywhile the samples shown for the Secretory and Normal-like subtypes havenormal histology (Magnification 200×).

FIGS. 2A-2D demonstrate that phenotypic associations with the molecularsubtypes are confirmed in an independent sample set. (FIG. 2A) The 190DC biopsies and the 3,936 genes were used to build a 22-gene nearestcentroid molecular subtype classifier. Semi-supervised hierarchalclustering of z-score normalized gene expression across the 22classifier genes and 190 DC biopsies training samples. (FIG. 2B) The22-gene nearest centroid molecular subtype classifier was used topredict the molecular subtypes of the 105 VC biopsies. Semi-supervisedhierarchal clustering of z-score normalized gene expression across 22genes and 105 VC is plotted. The rows of the heatmap give the gene nameand module membership, and the column color bar shows molecular subtypemembership. (FIG. 2C) Bubbleplots showing significant associations(p<0.01 by Fisher's Exact Test) between the VC molecular subtypes andsmoking status, biopsy histological grade, and the predicted LUSC tumormolecular subtypes. The columns represent the 4 molecular subtypes(Proliferative, Inflammatory, Secretory, and Normal) and the radius ofthe circle is proportional to the number of samples within each subtypethat have the row phenotype. (FIG. 2D) Bubbleplots showing significantassociations (p<0.01 by Fisher's Exact Test) between the VC molecularsubtypes and smoking status, biopsy histological grade, and thepredicted LUSC tumor molecular subtypes. The columns represent the 4molecular subtypes (Proliferative, Inflammatory, Secretory, andNormal-like) and the radius of the circle is proportional to the numberof samples within each subtype that have the row phenotype.

FIGS. 3A-3C demonstrate the performance of the molecular subtypeclassifier in the large airway brushes from normal appearing epitheliumsampled at the same time as the endobronchial biopsies. (FIG. 3A) The DC(left) and VC (right) cohorts, showing the number of brushes (y-axis)predicted to be positive for the Proliferative subtype that have atleast one biopsy (y-axis) with a classification of the Proliferativesubtype at the time the brush was sampled. (FIG. 3B) Boxplots of PC1 forModules 4, 5, 6, and 7 (y-axis) across the four molecular subtypes foreach cohort (x-axis). The asterisk indicates significant differencesbetween the Proliferative subtype versus all other samples (FDR<0.05).(FIG. 3C) Boxplots of PC1 for Modules 4, 5, 6, and 7 (y-axis) across thefour molecular subtypes for each cohort (x-axis). The asterisk indicatessignificant differences between the Proliferative subtype versus allother samples (FDR<0.05).

FIGS. 4A-4H demonstrate that the module enriched for interferonsignaling and antigen processing is associated with biopsyprogression/persistence and a depletion of innate and adaptive immunecells in the Proliferative subtype. (FIGS. 4A and 4F) Metageneexpression of Module 9 genes among DC biopsies within the Proliferativesubtype (p=0.002 between the progressive/persistent versus regressivebiopsies). Biopsy progression/regression was defined for each biopsybased on the histology of the biopsy and the worst histology recordedfor the same lung anatomic location in the future. Histology changesbetween normal, hyperplasia, and metaplasia were classified as “normalstable”, decreases in histological dysplasia grade or changes fromdysplastic histology to normal/hyperplasia/metaplasia were classified as“regressive”, lack of future histological data was classified as“unknown”, and everything else was classified as“progressive/persistent.” (FIGS. 4B and 4G) Boxplot of the percentagesof CD68 and CD163, CD68, CD163, CD4, and CD8 positively stained cellsbetween progressive/persistent and regressive biopsies (p<0.001 for allcomparisons). The x-axis labels indicate the number of regions (R)enumerated across (P) subjects for each stain and outcome group depictedin the boxplot. Biopsies were included in the analysis if their clinicaloutcome was concordant with the Module 9 score. (FIG. 4B) Metageneexpression of Module 9 genes among VC biopsies within the Proliferativesubtype (p=0.03 between the progressive/persistent versus regressivebiopsies). (FIG. 4C) Top: Z-score normalized gene expression across the112 genes in Module 9 and the DC biopsies (left) and the VC biopsies(right). Each heatmap is supervised according to the Module 9 GSVAscores. Top bars indicate the histological grade of the biopsies andtheir progression status. Bottom: xCell results indicating the relativeabundance of immune cell types across the DC biopsies (left) and the VCbiopsies (right). Immune cell types displayed are significantlyassociated with lesion progressive/persistence (FDR<0.05 in both the DCand VC after adjusting for differences in epithelial cell content).(FIG. 4D) Representative histology where the dashed line denoted theseparate of epithelium and stromal compartment Top panels: A progressivesevere dysplasia has reduced presence of immune cells demonstrated bythe marked reduction in expression of M2 macrophages (CD68/163 staining,double positive cells indicated by the arrows) and CD8 T cells. (samplecorresponds to *P in FIG. 4C.) Bottom panels: A regressive moderatedysplasia has increased presence of immune cells including M2macrophages (CD68/163 staining double positive cells indicated by thearrows) and CD8 T cells. (samples correspond to *R in FIG. 4C.) (FIGS.4E and 4H) Boxplots of the percentages of CD68 and CD163, CD68, CD163,CD4, and CD8 positively stained cells between progressive/persistent andregressive biopsies (p<0.001 for all comparisons). The x-axis labelsindicate the number of regions (R) enumerated across (P) subjects foreach stain and outcome group depicted in the boxplot. Biopsies wereincluded in the analysis if their clinical outcome was concordant withthe Module 9 score.

FIG. 5 depicts Batch Information and Alignment Statistics on Samples inboth the Discovery and Validation cohorts. Statistical tests between theDiscovery and Validation cohorts were performed using Fisher's ExactTest for categorical variables and Student's T-Test for continuousvariable. Percentages are reported for categorical variables and meanand standard deviations are reported for continuous variables.

FIG. 6 depicts a summary of Gene Modules. The module number, number ofgenes in the module, biological pathways and select genes associatedwith the module, and an FDR value for the difference in GSVA scores forthe module between the molecular subtypes are reported.

FIG. 7 depicts a List of Samples used for Immunofluorescence Studies.

FIG. 8 depicts the distribution of Molecular Subtypes by Subject. Thecolumns represent the 4 molecular subtypes (Proliferative, Inflammatory,Secretory, and Normal-like) and the radius of the circle is proportionalto the number of samples within each subtype.

FIG. 9 depicts a graph of Immunofluorescent Staining Quantitation ofProliferation, Basal Cell, and Ciliated Cell Markers across theMolecular Subtypes. Boxplot of immunofluorescent staining quantitationof KI67 (proliferation), KRT5 (basal cell) and TUB1A1 (ciliated cell)across representative samples from each molecular subtype (Proliferativen=4, Inflammatory n=3, Secretory n=1, Normal-like n=1). KI67 and KRT5staining are significantly higher in samples in the Proliferativesubtype (p=0.02 and p=0.01, respectively, for sample differences betweenthe Proliferative subtype and other subtypes). TUB1A1 was lower insamples in the Proliferative and Inflammatory subtypes but did not reachstatistical significance (p=0.07 for sample differences betweenProliferative and Inflammatory subtypes versus Inflammatory andSecretory subtypes).

FIGS. 10A-10H depict boxplots of Select Genes and Cell TypeDeconvolution Results across the Discovery and Validation Cohorts byMolecular Subtype. (FIGS. 10A-10D) Discovery cohort biopsies. (FIGS.10E-10H) Validation cohort biopsies. (FIG. 10A) and (FIG. 10E) showboxplots of gene expression levels of LUSC driver genes identified byTCGA across the molecular subtypes. (FIG. 10B) and (FIG. 10F) showboxplots of gene expression levels of cell type marker genes across themolecular subtypes. (FIG. 10C) and (FIG. 10G) show boxplots of GSVAscores calculated using Dvorak et al. gene sets across the molecularsubtypes. (FIG. 10D) and (FIG. 10H) show boxplots of ESTIMATE algorithmscores across the molecular subtypes. The ESTIMATE algorithm estimatesthe stromal (StromalScore), immune (ImmuneScore), and epithelial(ESTIMATEScore) cell fractions in each sample. High immune and stromalscores indicate a high fraction of stromal and immune cells while lowepithelial scores indicate a high fraction of epithelial cells.

FIG. 11 depicts a heatmap of the 22-gene Molecular Subtype Classifier inthe Discovery and Validation Cohort Biopsies. Semi-supervised hierarchalclustering of z-score normalized residual gene expression across the 22classifier genes and 190 DC biopsies training samples (left) and the 105VC biopsies (right). The rows of the heatmap show the gene modulemembership. The first column color bar shows molecular subtypemembership in the DC and the 22-gene predict subtype membership in theVC. The second column color bar depicts correct and incorrectpredictions in the DC using the 22-gene classifier and molecularsubtypes derived by performing consensus clustering across the VC.

FIG. 12 depicts graphs of gene module behavior across the MolecularSubtypes in the Discovery and Validation Cohort Biopsies. The mean ofthe first principal component calculated across module genes is plottedfor each molecular subtype.

FIG. 13 depicts the concordance between Module 9 and two Cell TypeDeconvolution Analyses. Top: Hierarchal clustering of z-score normalizedgene expression across the 112 genes in module 9 and the DC biopsies(left) and the VC biopsies (right). Each heatmap is supervised accordingto the module 9 GSVA scores. Top bars indicate the histological grade ofthe biopsies and their progression status. xCell results (Middle) andGSVA scores for gene sets described by Bindea et al. (Bottom) indicatingthe relative abundance of immune cell types across the DC biopsies(left) and the VC biopsies (right). Immune cell types displayed aresignificantly associated with lesion progression/persistence (FDR<0.05in both the DC and VC).

FIG. 14 depicts a tracheobronchial map of the locations of the sitessampled by endobronchial biopsy.

FIG. 15 depicts the distribution of subject among the discovery cohortendobronchial biopsies across the four molecular subtypes. Genes(n=3,936) organized into 9 gene co-expression modules were used todiscover four molecular subtypes (Proliferative, Inflammatory,Secretory, and Normal-like) across the 190 discovery cohort (DC)biopsies using consensus clustering. The heatmap shows semi-supervisedhierarchal clustering of z-score normalized gene expression across the3,936 genes and 190 DC biopsies. The top color bars represent thesubject the sample was derived and molecular subtype membership:Proliferative (n=52 samples), Inflammatory (n=37 samples), Secretory(n=61 samples), and Normal-like (n=40 samples). On the left side of theheatmap, the mean module GSVA score is plotted for each subtype.

FIG. 16 depicts the molecular subtype distribution for each subjectacross bronchoscopy procedures. The barplot shows for each subject andeach bronchoscopy procedure the number of biopsies sampled and theircorresponding molecular subtype. The y-axis indicates the subject numberand whether or not that subject had a prior history of either lungsquamous cell carcinoma (LUSC) or another type of lung cancer (Other).The discovery cohort includes subjects 1 through 32 and the validationcohort includes subjects 33 through 52. We did not detect a differencein the diversity of subtype classifications within a subject based onprior history of lung cancer (mean Shannon entropy of subtypeclassifications within patients with a history of lung cancer=1.12, n=32vs. patients without a history of lung cancer=1.25, n=17; Wilcoxon RankSum test p-value=0.43).

DETAILED DESCRIPTION

As described herein, the inventors have discovered that premalignantlesions in the airway of a subject can be characterized as being one offive: types: normal-like, secretory, inflammatory, progressiveproliferative, and persistent proliferative. Identifying thepremalignant lesion as one of these types permits more effectivetreatment of the subject, as different types of lesions will beresponsive to different treatments and require different treatment andmonitoring regimes. Accordingly, provided herein are methods oftreatment relating to the treatment of bronchial premalignant lesions ina subject. Such methods can comprise assays, tests, and/oridentification of the lesion type and administration of therapeuticregimens appropriate for that lesion type.

As used herein, “premalignant lesion” refers to an epithelial lesion ordysplasia which is a precursor or can be a precursor to cancer. Thebasement membrane is intact with no possibility of metastatic spread, asopposed to cancer. A bronchial premalignant lesion is a premalignantlesion present in the bronchial epithelium of a subject. Bronchialpremalignant lesions are typically small and can be difficult tovisualize using conventional white light bronchoscopy.

The bronchial premalignant lesions can exhibit one of five phenotypesdescribed herein, namely progressive proliferative, persistentproliferative, secretory, inflammatory, and normal-like. The subtypenames reference the key differences in molecular pathway activity whichdifferentiate the subtypes from each other. The different phenotypes oflesion can be distinguished from each other and from normal tissue byuse of the gene expression patterns described herein. As explained indetail elsewhere herein, the gene expression patterns identified hereinrelate to 10 modules of genes, where each module is a group of geneswith similar expression patterns across the different bronchialpremalignant lesion subtypes. The identity of each of the modules, e.g.the genes that comprise each module, are provided in Table 13 herein.Briefly, proliferative lesions (both progressive and persistent) aredistinguished by having increased module 4, 5, and 7 expression anddecreased module 6 expression. Progressive proliferative lesions can bedistinguished from persistent proliferative lesions in that they havedecreased module 9 expression and/or increased module 10 expression.Secretory lesions are distinguished by an increase in module 6expression and a decrease in module 1 expression and optionally, anincrease in module 8 expression and a decrease in modules 2, 5, and 7expression. Normal-like subtype is distinguished by an increase inmodule 6 expression and a decrease in module 9 expression andoptionally, an increase in module 1 expression and a decrease in module8 expression.

Standard treatment for subjects at risk of lung cancer, or who have beenidentified to have bronchial premalignant lesions, is annual screeningfor lung cancer (e.g. a bronchoscopy and/or chest CT scan). When asubject has a proliferative bronchial premalignant lesion, suchtreatment is no longer sufficient and the subject should be treated moreaggressively. Accordingly, in one aspect of any of the embodiments,provided herein is a method of treating bronchial premalignant lesions,the method comprising administering at least one of: i) both abronchoscopy-based procedure to survey the central airway and a chest CTscan; ii) at least every 6 months, at least one of a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; and/or iii)at least one anti-proliferative drug to a subject determined to have atleast one of a) an increased level of expression of at least one module5 gene as compared to a reference level; and b) a decreased level ofexpression of at least one module 6 gene as compared to a referencelevel. In one aspect of any of the embodiments, provided herein is amethod of treating bronchial premalignant lesions, the method comprisingdetermining a subject as to have at least one of a) an increased levelof expression of at least one module 5 gene as compared to a referencelevel; and b) a decreased level of expression of at least one module 6gene as compared to a reference level and administering at least one of:i) both a bronchoscopy-based procedure to survey the central airway anda chest CT scan; ii) at least about every 6 months (e.g., at least every1, 2, 3, 4, 5, or 6 months), at least one of a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; and/or iii)at least one anti-proliferative drug to the subject. In some embodimentsof any of the aspects, the reference level is a non-proliferativereference level.

In some embodiments, if the subject is determined not to have at leastone of a) an increased level of expression of at least one module 5 geneas compared to a reference level; and b) a decreased level of expressionof at least one module 6 gene as compared to a reference level, thesubject is not administered an anti-proliferative drug and isadministered a bronchoscopy-based procedure to survey the central airwayand/or a chest CT scan no more frequently than every 6 months (e.g., nomore frequently than every 6, 7, 8, 9, 10, 11, or 12 months). In someembodiments, if the subject is determined not to have a) an increasedlevel of expression of at least one module 5 gene as compared to areference level; and b) a decreased level of expression of at least onemodule 6 gene as compared to a reference level, the subject is notadministered an anti-proliferative drug and is administered abronchoscopy-based procedure to survey the central airway and/or a chestCT scan no more frequently than every 6 months (e.g., no more frequentlythan every 6, 7, 8, 9, 10, 11, or 12 months).

Module 5 and 6 gene expression, in a bronchial brushing sample, issufficient to identify a subject having a proliferative subtype lesion.This avoids the need to visualize and/or sample the actual lesion.Accordingly, in one aspect of any of the embodiments, provided herein isa method of treating bronchial premalignant lesions, the methodcomprising administering at least one of: i) both a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; ii) at leastevery 6 months, at least one of a bronchoscopy-based procedure to surveythe central airway and a chest CT scan; and/or iii) at least oneanti-proliferative drug to a subject determined to have, in a bronchialbrushing sample, a) an increased level of expression of at least onemodule 5 gene as compared to a reference level; and b) a decreased levelof expression of at least one module 6 gene as compared to a referencelevel. In one aspect of any of the embodiments, provided herein is amethod of treating bronchial premalignant lesions, the method comprisingdetermining a subject to have, in a bronchial brushing sample obtainedfrom the subject, a) an increased level of expression of at least onemodule 5 gene as compared to a reference level; and b) a decreased levelof expression of at least one module 6 gene as compared to a referencelevel and administering at least one of: i) both a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; ii) at leastevery 6 months, at least one of a bronchoscopy-based procedure to surveythe central airway and a chest CT scan; and/or iii) at least oneanti-proliferative drug to the subject. In some embodiments of any ofthe aspects, the reference level is a non-proliferative reference level.In some embodiments of any of the aspects, the bronchial brushing istaken from a morphologically-normal location in the right or leftmainstem bronchus. In some embodiments of any of the aspects, thebronchial brushing is taken from a visually-normal location in the rightor left mainstem bronchus.

Module 5 and 6 genes are provided in Table 13. The at least one module 5gene and/or module 6 gene can be any one or more of the module 5 and 6genes listed in Table 13.

In some embodiments of any of the aspects, the level of expression of atleast one module 5 gene or at least one module 6 gene is determined. Insome embodiments of any of the aspects, the level of expression of twoor more module 5 genes or two or more module 6 genes is determined. Insome embodiments of any of the aspects, the level of expression of eachmodule 5 gene or each module 6 gene of Table 13 is determined.

In some embodiments of any of the aspects, the level of expression of atleast one module 5 gene and at least one module 6 gene is determined. Insome embodiments of any of the aspects, the level of expression of twoor more module 5 genes and two or more module 6 genes is determined. Insome embodiments of any of the aspects, the level of expression of eachmodule 5 gene and each module 6 gene of Table 13 is determined.

In some embodiments of any of the aspects, the at least one module 5gene comprises or is RACGAP1 or TPX2. In some embodiments of any of theaspects, the at least one module 5 gene comprises or is RACGAP1 andTPX2. In some embodiments of any of the aspects, the at least one module6 gene comprises or is NEK11 or IFT88. In some embodiments of any of theaspects, the at least one module 6 gene comprises or is NEK11 and IFT88.

The proliferative subtype is further distinguished by increasedexpression of module 7 and/or 4. Accordingly, in some embodiments of anyof the aspects, the subject is further determined to have an increasedlevel of expression of at least one module 7 or module 4 gene ascompared to a reference level. In some embodiments of any of theaspects, the subject is further determined to have an increased level ofexpression of at least one module 7 and at least one module 4 gene ascompared to a reference level. In some embodiments of any of theaspects, the reference level is a non-proliferative reference level.

Module 4 and 7 genes are provided in Table 13. The at least one module 4gene and/or module 7 gene can be any one or more of the module 4 and 7genes listed in Table 13.

In some embodiments of any of the aspects, the level of expression of atleast one module 4 gene or at least one module 7 gene is determined. Insome embodiments of any of the aspects, the level of expression of twoor more module 4 genes or two or more module 7 genes is determined. Insome embodiments of any of the aspects, the level of expression of eachmodule 4 gene or each module 7 gene of Table 13 is determined.

In some embodiments of any of the aspects, the level of expression of atleast one module 4 gene and at least one module 7 gene is determined. Insome embodiments of any of the aspects, the level of expression of twoor more module 4 genes and two or more module 7 genes is determined. Insome embodiments of any of the aspects, the level of expression of eachmodule 4 gene and each module 7 gene of Table 13 is determined.

In some embodiments of any of the aspects, the at least one module 4gene comprises or is COX6A1 or COX7A2. In some embodiments of any of theaspects, the at least one module 4 gene comprises or is COX6A1 andCOX7A2. In some embodiments of any of the aspects, the at least onemodule 7 gene comprises or is RPL26 or RPL23. In some embodiments of anyof the aspects, the at least one module 7 gene comprises or is RPL26 andRPL23.

When a subject has a progressive proliferative bronchial premalignantlesion, aggressive treatment, even beyond that provided forproliferative bronchial premalignant lesion, can be indicated.Accordingly, in one aspect of any of the embodiments, provided herein isa method of treating bronchial premalignant lesions, the methodcomprising administering at least one of: i) both a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; ii) at leastevery 6 months, at least one of a bronchoscopy-based procedure to surveythe central airway and a chest CT scan; iii) at least one immunestimulating drug and/or iv) at least one immune stimulating drug and atleast one anti-proliferative drug to a subject determined to have adecreased level of expression of at least one module 9 gene as comparedto a reference level and/or an increased level of expression of at leastone module 10 gene as compared to a reference level. In one aspect ofany of the embodiments, provided herein is a method of treatingbronchial premalignant lesions, the method comprising a) determining asubject as to have a decreased level of expression of at least onemodule 9 gene as compared to a reference level and/or an increased levelof expression of at least one module 10 gene as compared to a referencelevel and b) administering at least one of: i) both a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; ii) at leastevery 6 months, at least one of a bronchoscopy-based procedure to surveythe central airway and a chest CT scan; iii) at least one immunestimulating drug and/or iv) at least one immune stimulating drug and atleast one anti-proliferative drug to the subject. In some embodiments ofany of the aspects, the reference level is a non-proliferative referencelevel. In some embodiments of any of the aspects, the bronchoscopy-basedprocedure further comprises biopsy of the lesions to remove abnormaltissue.

In some embodiments, if the subject is determined not to have adecreased level of expression of at least one module 9 gene as comparedto a reference level and/or not to have an increased level of expressionof at least one module 10 gene as compared to a reference level, thesubject i) is not administered an immune stimulating drug, ii) is notadministered both an immune stimulating drug and an anti-proliferativedrug, iii) is administered a bronchoscopy-based procedure and/or a chestCT scan no more frequently than every 6 months (e.g., no more frequentlythan every 6, 7, 8, 9, 10, 11, or 12 months), and/or iv) is notadministered a bronchoscopy-based procedure to biopsy lesions to removeabnormal tissue.

Module 9 genes are provided in Table 13. The at least one module 9 genecan be any one or more of the module 9 genes listed in Table 13. Module9 genes are provided in Table 16. The at least one module 9 gene can beany one or more of the module 9 genes listed in Table 16.

In some embodiments of any of the aspects, the level of expression oftwo or more module 9 gene is determined. In some embodiments of any ofthe aspects, the level of expression of each module 9 gene of Table 13is determined. In some embodiments of any of the aspects, the level ofexpression of each module 9 gene of Table 16 is determined.

In some embodiments of any of the aspects, the at least one module 9gene comprises or is EPSTI1; UBE2L6; B2M and/or TAP1. In someembodiments of any of the aspects, the at least one module 9 genecomprises or is EPSTI1; UBE2L6; B2M; and TAP1. In some embodiments ofany of the aspects, the at least one module 9 gene comprises or is apairwise combination of any of:

EPSTI1 and UBE2L6 EPSTI1 and B2M EPSTI1 and TAP1 UBE2L6 and B2M UBE2L6and TAP1 B2M and TAP1

In some embodiments of any of the aspects, the at least one module 9gene comprises or is a three-way combination of any of:

EPSTI1; UBE2L6; and B2M EPSTI1; UBE2L6; and TAP1 EPSTI1; B2M; and TAP1TAP1; UBE2L6; and B2M

Module 10 genes are provided in Table 13. The at least one module 10gene can be any one or more of the module 9 genes listed in Table 13. Insome embodiments of any of the aspects, the level of expression of bothmodule 10 genes is determined. In some embodiments of any of theaspects, the at least one module 10 gene comprises or is CACNB3 orMAPK10. In some embodiments of any of the aspects, the at least onemodule 10 gene comprises or is CACNB3 and MAPK10.

When a subject has an inflammatory bronchial premalignant lesionaggressive and/or anti-inflammatory treatment can be beneficial.Accordingly, in one aspect of any of the embodiments, provided herein isa method of treating bronchial premalignant lesions, the methodcomprising administering at least one of: i) both a bronchoscopy-basedprocedure to survey the central airway and a chest CT scan; ii) at leastevery 6 months, at least one of a bronchoscopy-based procedure to surveythe central airway and a chest CT scan; and/or iii) at least oneanti-inflammatory drug to a subject determined to have at least one ofa) an increased level of expression of at least one module 2 gene ascompared to a reference level; and b) a decreased level of expression ofat least one module 6 gene as compared to a reference level. In oneaspect of any of the embodiments, provided herein is a method oftreating bronchial premalignant lesions, the method comprisingdetermining a subject as to have at least one of a) an increased levelof expression of at least one module 2 gene as compared to a referencelevel; and b) a decreased level of expression of at least one module 6gene as compared to a reference level and administering at least one of:i) both a bronchoscopy-based procedure to survey the central airway anda chest CT scan; ii) at least every 6 months, at least one of abronchoscopy-based procedure to survey the central airway and a chest CTscan; and/or iii) at least one anti-inflammatory drug to the subject. Insome embodiments of any of the aspects, the reference level is anon-inflammatory reference level.

In some embodiments, if the subject is determined not to have at leastone of a) an increased level of expression of at least one module 2 geneas compared to a reference level; and b) a decreased level of expressionof at least one module 6 gene as compared to a reference level, thesubject is not administered an anti-inflammatory drug and isadministered a bronchoscopy-based procedure to survey the central airwayand/or a chest CT scan no more frequently than every 6 months (e.g., nomore frequently than every 6, 7, 8, 9, 10, 11, or 12 months). In someembodiments, if the subject is determined not to have a) an increasedlevel of expression of at least one module 2 gene as compared to areference level; and b) a decreased level of expression of at least onemodule 6 gene as compared to a reference level, the subject is notadministered an anti-inflammatory drug and is administered abronchoscopy-based procedure to survey the central airway and/or a chestCT scan no more frequently than every 6 months (e.g., no more frequentlythan every 6, 7, 8, 9, 10, 11, or 12 months).

Module 2 and 6 genes are provided in Table 13. The at least one module 2gene and/or module 6 gene can be any one or more of the module 5 and 6genes listed in Table 13.

In some embodiments of any of the aspects, the level of expression of atleast one module 2 gene or at least one module 6 gene is determined. Insome embodiments of any of the aspects, the level of expression of twoor more module 2 genes or two or more module 6 genes is determined. Insome embodiments of any of the aspects, the level of expression of eachmodule 2 gene or each module 6 gene of Table 13 is determined.

In some embodiments of any of the aspects, the level of expression of atleast one module 2 gene and at least one module 6 gene is determined. Insome embodiments of any of the aspects, the level of expression of twoor more module 2 genes and two or more module 6 genes is determined. Insome embodiments of any of the aspects, the level of expression of eachmodule 2 gene and each module 6 gene of Table 13 is determined.

In some embodiments of any of the aspects, the at least one module 2gene comprises or is MSANTD2, CCNL2, or LUC7L. In some embodiments ofany of the aspects, the at least one module 2 gene comprises or isMSANTD2 and LUC7L. In some embodiments of any of the aspects, the atleast one module 2 gene comprises or is MSANTD2 and CCNL2. In someembodiments of any of the aspects, the at least one module 2 genecomprises or is CCNL2 and LUC7L. In some embodiments of any of theaspects, the at least one module 2 gene comprises or is MSANTD2, CCNL2,and LUC7L. In some embodiments of any of the aspects, the at least onemodule 6 gene comprises or is NEK11 or IFT88. In some embodiments of anyof the aspects, the at least one module 6 gene comprises or is NEK11 andIFT88.

The inflammatory subtype is further distinguished by increasedexpression of module 7, 1 and/or 8 and/or decreased expression of module4 and/or 5. Accordingly, in some embodiments of any of the aspects, thesubject is further determined to have at least one of: i) an increasedlevel of expression of at least one module 7, module 1, and/or or module8 gene, and ii) a decreased level of expression of at least one module 4or module 5 gene as compared to a reference level. In some embodimentsof any of the aspects, the subject is further determined to have atleast one of: i) an increased level of expression of at least one module7, module 1, and/or or module 8 gene, and ii) a decreased level ofexpression of at least one module 4 or module 5 gene as compared to areference level. In some embodiments of any of the aspects, thereference level is a non-inflammatory reference level.

Module 7, 1, 8, 4 and 5 genes are provided in Table 13. The at least onemodule 7, 1, 8, 4, and/or 5 gene can be any one or more of the module 7,1, 8, 4, and/or 5 genes listed in Table 13. In some embodiments of anyof the aspects, the level of expression of each module 7, 1, 8, 4 and/or5 gene of Table 13 is determined. In some embodiments of any of theaspects, the level of expression of each module 7, 1, 8, 4 and 5 gene ofTable 13 is determined.

In some embodiments of any of the aspects, the at least one module 4gene comprises or is COX6A1 or COX7A2. In some embodiments of any of theaspects, the at least one module 4 gene comprises or is COX6A1 andCOX7A2. In some embodiments of any of the aspects, the at least onemodule 7 gene comprises or is RPL26 or RPL23. In some embodiments of anyof the aspects, the at least one module 7 gene comprises or is RPL26 andRPL23. In some embodiments of any of the aspects, the at least onemodule 5 gene comprises or is RACGAP1 or TPX2. In some embodiments ofany of the aspects, the at least one module 5 gene comprises or isRACGAP1 and TPX2. In some embodiments of any of the aspects, the atleast one module 1 gene comprises or is KIRREL; PHLDB1; or MARVELD1. Insome embodiments of any of the aspects, the at least one module 1 genecomprises or is PHLDB1 and MARVELD1. In some embodiments of any of theaspects, the at least one module 1 gene comprises or is KIRREL andPHLDB1. In some embodiments of any of the aspects, the at least onemodule 1 gene comprises or is KIRREL and MARVELD1. In some embodimentsof any of the aspects, the at least one module 1 gene comprises or isKIRREL; PHLDB1; and MARVELD1. In some embodiments of any of the aspects,the at least one module 8 gene comprises or is DCO2; CD53; or LAPTM. Insome embodiments of any of the aspects, the at least one module 8 genecomprises or is CD53 and LAPTM. In some embodiments of any of theaspects, the at least one module 8 gene comprises or is DCO2 and CD53.In some embodiments of any of the aspects, the at least one module 8gene comprises or is DCO2 and LAPTM. In some embodiments of any of theaspects, the at least one module 8 gene comprises or is DCO2; CD53; andLAPTM.

In some embodiments of any of the aspects, the level of expression ofeach of the genes of Table 15 is determined. In some embodiments of anyof the aspects, the level of expression of each of the genes of Table 15in a bronchial brushing sample is determined.

In some embodiments of any of the aspects, the level of expression ofeach of the genes of Table 14 is determined. In some embodiments of anyof the aspects, the level of expression of each of the genes of Table 14in a bronchial brushing sample is determined.

In some embodiments of any of the aspects, the methods described hereincan further comprise determining the level of expression of any of thefollowing genes: SOX2, NFE2L2, PIK3CA (which are squamous cancer markergenes), KRT5, MUC5AC, TUB1A1, SCGB1A1, and FOXK1 (which are epithelialmarker genes).

As described herein, levels of gene expression can be modulated (e.g.,increased or decreased) in subjects with premalignant lesions ofdifferent subtypes.

In some embodiments of any of the aspects, the method comprisesadministering a treatment described herein to a subject previouslydetermined to have an expression level(s) as described herein. In someembodiments of any of the aspects, described herein is a method oftreating bronchial premalignant lesions in a subject in need thereof,the method comprising: a) first determining the level of expression ofthe at least one gene in a sample obtained from a subject; and b) thenadministering a treatment as described herein to the subject if thelevel of expression of modulated relative to a reference in the mannerdescribed herein. In one aspect of any of the embodiments, describedherein is a method of treating bronchial premalignant lesions in asubject in need thereof, the method comprising: a) determining if thesubject has a modulation of a level of expression as described hereinand b) instructing or directing that the subject be administered theappropriate treatment described herein for the particular modulation ofexpression which has been determined.

In some embodiments of any of the aspects, the step of determining ifthe subject has modulation of an expression level can comprise i)obtaining or having obtained a sample from the subject and ii)performing or having performed an assay on the sample obtained from thesubject to determine/measure the level of expression in the subject. Insome embodiments of any of the aspects, the step of determining if thesubject has a modulation of a level of expression can compriseperforming or having performed an assay on a sample obtained from thesubject to determine/measure the level of expression in the subject. Insome embodiments of any of the aspects, the step of determining if thesubject has a modulation of a level of expression can comprise orderingor requesting an assay on a sample obtained from the subject todetermine/measure the level of expression in the subject. In someembodiments of any of the aspects, the step of determining if thesubject has a modulation of a level of expression can comprise receivingthe results of an assay on a sample obtained from the subject todetermine/measure the level of expression in the subject. In someembodiments of any of the aspects, the step of determining if thesubject has a modulation of a level of expression can comprise receivinga report, results, or other means of identifying the subject as asubject with a modulation of a level of expression.

In some embodiments of any of the aspects, the step of instructing ordirecting that the subject be administered a particular treatment cancomprise providing a report of the assay results. In some embodiments ofany of the aspects, the step of instructing or directing that thesubject be administered a particular treatment can comprise providing areport of the assay results and/or treatment recommendations in view ofthe assay results.

In some embodiments of any of the aspects, measurement of the level of atarget and/or detection of the level or presence of a target, e.g. of anexpression product (nucleic acid or polypeptide of one of the genesdescribed herein) or a mutation can comprise a transformation. As usedherein, the term “transforming” or “transformation” refers to changingan object or a substance, e.g., biological sample, nucleic acid orprotein, into another substance. The transformation can be physical,biological or chemical. Exemplary physical transformation includes, butis not limited to, pre-treatment of a biological sample, e.g., fromwhole blood to blood serum by differential centrifugation. Abiological/chemical transformation can involve the action of at leastone enzyme and/or a chemical reagent in a reaction. For example, a DNAsample can be digested into fragments by one or more restrictionenzymes, or an exogenous molecule can be attached to a fragmented DNAsample with a ligase. In some embodiments of any of the aspects, a DNAsample can undergo enzymatic replication, e.g., by polymerase chainreaction (PCR).

Transformation, measurement, and/or detection of a target molecule, e.g.a mRNA or polypeptide can comprise contacting a sample obtained from asubject with a reagent (e.g. a detection reagent) which is specific forthe target, e.g., a target-specific reagent. In some embodiments of anyof the aspects, the target-specific reagent is detectably labeled. Insome embodiments of any of the aspects, the target-specific reagent iscapable of generating a detectable signal. In some embodiments of any ofthe aspects, the target-specific reagent generates a detectable signalwhen the target molecule is present.

Methods to measure gene expression products are known to a skilledartisan. Such methods to measure gene expression products, e.g., proteinlevel, include ELISA (enzyme linked immunosorbent assay), western blot,immunoprecipitation, and immunofluorescence using detection reagentssuch as an antibody or protein binding agents. Alternatively, a peptidecan be detected in a subject by introducing into a subject a labeledanti-peptide antibody and other types of detection agent. For example,the antibody can be labeled with a detectable marker whose presence andlocation in the subject is detected by standard imaging techniques.

For example, antibodies for the various targets described herein arecommercially available and can be used for the purposes of the inventionto measure protein expression levels. Alternatively, since the aminoacid sequences for the targets described herein are known and publicallyavailable at the NCBI website, one of skill in the art can raise theirown antibodies against these polypeptides of interest for the purpose ofthe methods described herein.

The amino acid sequences of the polypeptides described herein have beenassigned NCBI and ENSBL accession numbers for different species such ashuman, mouse and rat. The sequences for any of the genes describedherein can be readily retrieved from either database by one of ordinaryskill in the art. In some embodiments of any of the aspects, thesequence of a gene, transcript, or polypeptide described herein is thesequence available in the NCBI or ENSMBL database as of the filing dateof this application.

In some embodiments of any of the aspects, immunohistochemistry (“IHC”)and immunocytochemistry (“ICC”) techniques can be used. IHC is theapplication of immunochemistry to tissue sections, whereas ICC is theapplication of immunochemistry to cells or tissue imprints after theyhave undergone specific cytological preparations such as, for example,liquid-based preparations. Immunochemistry is a family of techniquesbased on the use of an antibody, wherein the antibodies are used tospecifically target molecules inside or on the surface of cells. Theantibody typically contains a marker that will undergo a biochemicalreaction, and thereby experience a change of color, upon encounteringthe targeted molecules. In some instances, signal amplification can beintegrated into the particular protocol, wherein a secondary antibody,that includes the marker stain or marker signal, follows the applicationof a primary specific antibody.

In some embodiments of any of the aspects, the assay can be a Westernblot analysis. Alternatively, proteins can be separated bytwo-dimensional gel electrophoresis systems. Two-dimensional gelelectrophoresis is well known in the art and typically involvesiso-electric focusing along a first dimension followed by SDS-PAGEelectrophoresis along a second dimension. These methods also require aconsiderable amount of cellular material. The analysis of 2D SDS-PAGEgels can be performed by determining the intensity of protein spots onthe gel, or can be performed using immune detection. In otherembodiments, protein samples are analyzed by mass spectroscopy.

Immunological tests can be used with the methods and assays describedherein and include, for example, competitive and non-competitive assaysystems using techniques such as Western blots, radioimmunoassay (RIA),ELISA (enzyme linked immunosorbent assay), “sandwich” immunoassays,immunoprecipitation assays, immunodiffusion assays, agglutinationassays, e.g. latex agglutination, complement-fixation assays,immunoradiometric assays, fluorescent immunoassays, e.g. FIA(fluorescence-linked immunoassay), chemiluminescence immunoassays(CLIA), electrochemiluminescence immunoassay (ECLIA, countingimmunoassay (CIA), lateral flow tests or immunoassay (LFIA), magneticimmunoassay (MIA), and protein A immunoassays. Methods for performingsuch assays are known in the art, provided an appropriate antibodyreagent is available. In some embodiments of any of the aspects, theimmunoassay can be a quantitative or a semi-quantitative immunoassay.

An immunoassay is a biochemical test that measures the concentration ofa substance in a biological sample, typically a fluid sample such asblood or serum, using the interaction of an antibody or antibodies toits antigen. The assay takes advantage of the highly specific binding ofan antibody with its antigen. For the methods and assays describedherein, specific binding of the target polypeptides with respectiveproteins or protein fragments, or an isolated peptide, or a fusionprotein described herein occurs in the immunoassay to form a targetprotein/peptide complex. The complex is then detected by a variety ofmethods known in the art. An immunoassay also often involves the use ofa detection antibody.

Enzyme-linked immunosorbent assay, also called ELISA, enzyme immunoassayor EIA, is a biochemical technique used mainly in immunology to detectthe presence of an antibody or an antigen in a sample. The ELISA hasbeen used as a diagnostic tool in medicine and plant pathology, as wellas a quality control check in various industries.

In one embodiment, an ELISA involving at least one antibody withspecificity for the particular desired antigen (e.g., any of the targetsas described herein) can also be performed. A known amount of sampleand/or antigen is immobilized on a solid support (usually a polystyrenemicro titer plate). Immobilization can be either non-specific (e.g., byadsorption to the surface) or specific (e.g. where another antibodyimmobilized on the surface is used to capture antigen or a primaryantibody). After the antigen is immobilized, the detection antibody isadded, forming a complex with the antigen. The detection antibody can becovalently linked to an enzyme, or can itself be detected by a secondaryantibody which is linked to an enzyme through bio-conjugation. Betweeneach step the plate is typically washed with a mild detergent solutionto remove any proteins or antibodies that are not specifically bound.After the final wash step the plate is developed by adding an enzymaticsubstrate to produce a visible signal, which indicates the quantity ofantigen in the sample. Older ELISAs utilize chromogenic substrates,though newer assays employ fluorogenic substrates with much highersensitivity.

In another embodiment, a competitive ELISA is used. Purified antibodiesthat are directed against a target polypeptide or fragment thereof arecoated on the solid phase of multi-well plate, i.e., conjugated to asolid surface. A second batch of purified antibodies that are notconjugated on any solid support is also needed. These non-conjugatedpurified antibodies are labeled for detection purposes, for example,labeled with horseradish peroxidase to produce a detectable signal. Asample (e.g., a blood sample) from a subject is mixed with a knownamount of desired antigen (e.g., a known volume or concentration of asample comprising a target polypeptide) together with the horseradishperoxidase labeled antibodies and the mixture is then are added tocoated wells to form competitive combination. After incubation, if thepolypeptide level is high in the sample, a complex of labeled antibodyreagent-antigen will form. This complex is free in solution and can bewashed away. Washing the wells will remove the complex. Then the wellsare incubated with TMB (3, 3′, 5, 5′-tetramethylbenzidene) colordevelopment substrate for localization of horseradishperoxidase-conjugated antibodies in the wells. There will be no colorchange or little color change if the target polypeptide level is high inthe sample. If there is little or no target polypeptide present in thesample, a different complex in formed, the complex of solid supportbound antibody reagents-target polypeptide. This complex is immobilizedon the plate and is not washed away in the wash step. Subsequentincubation with TMB will produce significant color change. Such acompetitive ELSA test is specific, sensitive, reproducible and easy tooperate.

There are other different forms of ELISA, which are well known to thoseskilled in the art. The standard techniques known in the art for ELISAare described in “Methods in Immunodiagnosis”, 2nd Edition, Rose andBigazzi, eds. John Wiley & Sons, 1980; and Oellerich, M. 1984, J. Clin.Chem. Clin. Biochem. 22:895-904. These references are herebyincorporated by reference in their entirety.

In one embodiment, the levels of a polypeptide in a sample can bedetected by a lateral flow immunoassay test (LFIA), also known as theimmunochromatographic assay, or strip test. LFIAs are a simple deviceintended to detect the presence (or absence) of antigen, e.g. apolypeptide, in a fluid sample. There are currently many LFIA tests usedfor medical diagnostics, either for home testing, point of care testing,or laboratory use. LFIA tests are a form of immunoassay in which thetest sample flows along a solid substrate via capillary action. Afterthe sample is applied to the test strip it encounters a colored reagent(generally comprising antibody specific for the test target antigen)bound to microparticles which mixes with the sample and transits thesubstrate encountering lines or zones which have been pretreated withanother antibody or antigen. Depending upon the level of targetpolypeptides present in the sample the colored reagent can be capturedand become bound at the test line or zone. LFIAs are essentiallyimmunoassays adapted to operate along a single axis to suit the teststrip format or a dipstick format. Strip tests are extremely versatileand can be easily modified by one skilled in the art for detecting anenormous range of antigens from fluid samples such as urine, blood,water, and/or homogenized tissue samples etc. Strip tests are also knownas dip stick tests, the name bearing from the literal action of“dipping” the test strip into a fluid sample to be tested. LFIA striptests are easy to use, require minimum training and can easily beincluded as components of point-of-care test (POCT) diagnostics to beuse on site in the field. LFIA tests can be operated as eithercompetitive or sandwich assays. Sandwich LFIAs are similar to sandwichELISA. The sample first encounters colored particles which are labeledwith antibodies raised to the target antigen. The test line will alsocontain antibodies to the same target, although it may bind to adifferent epitope on the antigen. The test line will show as a coloredband in positive samples. In some embodiments of any of the aspects, thelateral flow immunoassay can be a double antibody sandwich assay, acompetitive assay, a quantitative assay or variations thereof.Competitive LFIAs are similar to competitive ELISA. The sample firstencounters colored particles which are labeled with the target antigenor an analogue. The test line contains antibodies to the target/itsanalogue. Unlabelled antigen in the sample will block the binding siteson the antibodies preventing uptake of the colored particles. The testline will show as a colored band in negative samples. There are a numberof variations on lateral flow technology. It is also possible to applymultiple capture zones to create a multiplex test.

The use of “dip sticks” or LFIA test strips and other solid supportshave been described in the art in the context of an immunoassay for anumber of antigen biomarkers. U.S. Pat. Nos. 4,943,522; 6,485,982;6,187,598; 5,770,460; 5,622,871; 6,565,808, U.S. patent application Ser.No. 10/278,676; U.S. Ser. No. 09/579,673 and U.S. Ser. No. 10/717,082,which are incorporated herein by reference in their entirety, arenon-limiting examples of such lateral flow test devices. Examples ofpatents that describe the use of “dip stick” technology to detectsoluble antigens via immunochemical assays include, but are not limitedto U.S. Pat. Nos. 4,444,880; 4,305,924; and 4,135,884; which areincorporated by reference herein in their entireties. The apparatusesand methods of these three patents broadly describe a first componentfixed to a solid surface on a “dip stick” which is exposed to a solutioncontaining a soluble antigen that binds to the component fixed upon the“dip stick,” prior to detection of the component-antigen complex uponthe stick. It is within the skill of one in the art to modify theteachings of this “dip stick” technology for the detection ofpolypeptides using antibody reagents as described herein.

Other techniques can be used to detect the level of a polypeptide in asample. One such technique is the dot blot, an adaptation of Westernblotting (Towbin et at., Proc. Nat. Acad. Sci. 76:4350 (1979)). In aWestern blot, the polypeptide or fragment thereof can be dissociatedwith detergents and heat, and separated on an SDS-PAGE gel before beingtransferred to a solid support, such as a nitrocellulose or PVDFmembrane. The membrane is incubated with an antibody reagent specificfor the target polypeptide or a fragment thereof. The membrane is thenwashed to remove unbound proteins and proteins with non-specificbinding. Detectably labeled enzyme-linked secondary or detectionantibodies can then be used to detect and assess the amount ofpolypeptide in the sample tested. A dot blot immobilizes a proteinsample on a defined region of a support, which is then probed withantibody and labelled secondary antibody as in Western blotting. Theintensity of the signal from the detectable label in either formatcorresponds to the amount of enzyme present, and therefore the amount ofpolypeptide. Levels can be quantified, for example by densitometry.

In some embodiments of any of the aspects, the level of a target can bemeasured, by way of non-limiting example, by Western blot;immunoprecipitation; enzyme-linked immunosorbent assay (ELISA);radioimmunological assay (RIA); sandwich assay; fluorescence in situhybridization (FISH); immunohistological staining; radioimmunometricassay; immunofluoresence assay; mass spectroscopy and/orimmunoelectrophoresis assay.

In certain embodiments, the gene expression products as described hereincan be instead determined by determining the level of messenger RNA(mRNA) expression of the genes described herein. Such molecules can beisolated, derived, or amplified from a biological sample, such as ablood sample. Techniques for the detection of mRNA expression is knownby persons skilled in the art, and can include but not limited to, PCRprocedures, RT-PCR, quantitative RT-PCR Northern blot analysis,differential gene expression, RNAse protection assay, microarray basedanalysis, next-generation sequencing; hybridization methods, etc.

In general, the PCR procedure describes a method of gene amplificationwhich is comprised of (i) sequence-specific hybridization of primers tospecific genes or sequences within a nucleic acid sample or library,(ii) subsequent amplification involving multiple rounds of annealing,elongation, and denaturation using a thermostable DNA polymerase, and(iii) screening the PCR products for a band of the correct size. Theprimers used are oligonucleotides of sufficient length and appropriatesequence to provide initiation of polymerization, i.e. each primer isspecifically designed to be complementary to a strand of the genomiclocus to be amplified. In an alternative embodiment, mRNA level of geneexpression products described herein can be determined byreverse-transcription (RT) PCR and by quantitative RT-PCR (QRT-PCR) orreal-time PCR methods. Methods of RT-PCR and QRT-PCR are well known inthe art.

In some embodiments of any of the aspects, the level of an mRNA can bemeasured by a quantitative sequencing technology, e.g. a quantitativenext-generation sequence technology. Methods of sequencing a nucleicacid sequence are well known in the art. Briefly, a sample obtained froma subject can be contacted with one or more primers which specificallyhybridize to a single-strand nucleic acid sequence flanking the targetgene sequence and a complementary strand is synthesized. In somenext-generation technologies, an adaptor (double or single-stranded) isligated to nucleic acid molecules in the sample and synthesis proceedsfrom the adaptor or adaptor compatible primers. In some third-generationtechnologies, the sequence can be determined, e.g. by determining thelocation and pattern of the hybridization of probes, or measuring one ormore characteristics of a single molecule as it passes through a sensor(e.g. the modulation of an electrical field as a nucleic acid moleculepasses through a nanopore). Exemplary methods of sequencing include, butare not limited to, Sanger sequencing, dideoxy chain termination,high-throughput sequencing, next generation sequencing, 454 sequencing,SOLiD sequencing, polony sequencing, Illumina sequencing, Ion Torrentsequencing, sequencing by hybridization, nanopore sequencing, Helioscopesequencing, single molecule real time sequencing, RNAP sequencing, andthe like. Methods and protocols for performing these sequencing methodsare known in the art, see, e.g. “Next Generation Genome Sequencing” Ed.Michal Janitz, Wiley-VCH; “High-Throughput Next Generation Sequencing”Eds. Kwon and Ricke, Humanna Press, 2011; and Sambrook et al., MolecularCloning: A Laboratory Manual (4 ed.), Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y., USA (2012); which are incorporated byreference herein in their entireties.

The nucleic acid sequences of the genes described herein have beenassigned NCBI and ENSBL accession numbers for different species such ashuman, mouse and rat. The sequences for any of the genes describedherein can be readily retrieved from either database by one of ordinaryskill in the art. In some embodiments of any of the aspects, thesequence of a gene, transcript, or polypeptide described herein is thesequence available in the NCBI or ENSMBL database as of the filing dateof this application. Accordingly, a skilled artisan can design anappropriate primer based on the known sequence for determining the mRNAlevel of the respective gene.

Nucleic acid and ribonucleic acid (RNA) molecules can be isolated from aparticular biological sample using any of a number of procedures, whichare well-known in the art, the particular isolation procedure chosenbeing appropriate for the particular biological sample. For example,freeze-thaw and alkaline lysis procedures can be useful for obtainingnucleic acid molecules from solid materials; heat and alkaline lysisprocedures can be useful for obtaining nucleic acid molecules fromurine; and proteinase K extraction can be used to obtain nucleic acidfrom blood (Roiff, A et al. PCR: Clinical Diagnostics and Research,Springer (1994)).

In some embodiments of any of the aspects, one or more of the reagents(e.g. an antibody reagent and/or nucleic acid probe) described hereincan comprise a detectable label and/or comprise the ability to generatea detectable signal (e.g. by catalyzing reaction converting a compoundto a detectable product). Detectable labels can comprise, for example, alight-absorbing dye, a fluorescent dye, or a radioactive label.Detectable labels, methods of detecting them, and methods ofincorporating them into reagents (e.g. antibodies and nucleic acidprobes) are well known in the art.

In some embodiments of any of the aspects, detectable labels can includelabels that can be detected by spectroscopic, photochemical,biochemical, immunochemical, electromagnetic, radiochemical, or chemicalmeans, such as fluorescence, chemifluorescence, or chemiluminescence, orany other appropriate means. The detectable labels used in the methodsdescribed herein can be primary labels (where the label comprises amoiety that is directly detectable or that produces a directlydetectable moiety) or secondary labels (where the detectable label bindsto another moiety to produce a detectable signal, e.g., as is common inimmunological labeling using secondary and tertiary antibodies). Thedetectable label can be linked by covalent or non-covalent means to thereagent. Alternatively, a detectable label can be linked such as bydirectly labeling a molecule that achieves binding to the reagent via aligand-receptor binding pair arrangement or other such specificrecognition molecules. Detectable labels can include, but are notlimited to radioisotopes, bioluminescent compounds, chromophores,antibodies, chemiluminescent compounds, fluorescent compounds, metalchelates, and enzymes.

In other embodiments, the detection reagent is label with a fluorescentcompound. When the fluorescently labeled reagent is exposed to light ofthe proper wavelength, its presence can then be detected due tofluorescence. In some embodiments of any of the aspects, a detectablelabel can be a fluorescent dye molecule, or fluorophore including, butnot limited to fluorescein, phycoerythrin, phycocyanin, o-phthaldehyde,fluorescamine, Cy3™, Cy5™, allophycocyanine, Texas Red, perideninchlorophyll, cyanine, tandem conjugates such as phycoerythrin-Cy5™,green fluorescent protein, rhodamine, fluorescein isothiocyanate (FITC)and Oregon Green™, rhodamine and derivatives (e.g., Texas red andtetrarhodimine isothiocynate (TRITC)), biotin, phycoerythrin, AMCA,CyDyes™, 6-carboxyfhiorescein (commonly known by the abbreviations FAMand F), 6-carboxy-2′,4′,7′,4,7-hexachlorofiuorescein (HEX),6-carboxy-4′,5′-dichloro-2′,7′-dimethoxyfluorescein (JOE or J),N,N,N′,N′-tetramethyl-6carboxyrhodamine (TAMRA or T),6-carboxy-X-rhodamine (ROX or R), 5-carboxyrhodamine-6G (R6G5 or G5),6-carboxyrhodamine-6G (R6G6 or G6), and rhodamine 110; cyanine dyes,e.g. Cy3, Cy5 and Cy7 dyes; coumarins, e.g umbelliferone; benzimidedyes, e.g. Hoechst 33258; phenanthridine dyes, e.g. Texas Red; ethidiumdyes; acridine dyes; carbazole dyes; phenoxazine dyes; porphyrin dyes;polymethine dyes, e.g. cyanine dyes such as Cy3, Cy5, etc; BODIPY dyesand quinoline dyes. In some embodiments of any of the aspects, adetectable label can be a radiolabel including, but not limited to ³H,¹²⁵I, ³⁵S, ¹⁴C, ³²P, and ³³P. In some embodiments of any of the aspects,a detectable label can be an enzyme including, but not limited tohorseradish peroxidase and alkaline phosphatase. An enzymatic label canproduce, for example, a chemiluminescent signal, a color signal, or afluorescent signal. Enzymes contemplated for use to detectably label anantibody reagent include, but are not limited to, malate dehydrogenase,staphylococcal nuclease, delta-V-steroid isomerase, yeast alcoholdehydrogenase, alpha-glycerophosphate dehydrogenase, triose phosphateisomerase, horseradish peroxidase, alkaline phosphatase, asparaginase,glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase,glucose-VI-phosphate dehydrogenase, glucoamylase andacetylcholinesterase. In some embodiments of any of the aspects, adetectable label is a chemiluminescent label, including, but not limitedto lucigenin, luminol, luciferin, isoluminol, theromatic acridiniumester, imidazole, acridinium salt and oxalate ester. In some embodimentsof any of the aspects, a detectable label can be a spectral colorimetriclabel including, but not limited to colloidal gold or colored glass orplastic (e.g., polystyrene, polypropylene, and latex) beads.

In some embodiments of any of the aspects, detection reagents can alsobe labeled with a detectable tag, such as c-Myc, HA, VSV-G, HSV, FLAG,V5, HIS, or biotin. Other detection systems can also be used, forexample, a biotin-streptavidin system. In this system, the antibodiesimmunoreactive (i. e. specific for) with the biomarker of interest isbiotinylated. Quantity of biotinylated antibody bound to the biomarkeris determined using a streptavidin-peroxidase conjugate and achromogenic substrate. Such streptavidin peroxidase detection kits arecommercially available, e. g. from DAKO; Carpinteria, CA. A reagent canalso be detectably labeled using fluorescence emitting metals such as¹⁵²Eu, or others of the lanthanide series. These metals can be attachedto the reagent using such metal chelating groups asdiethylenetriaminepentaacetic acid (DTPA) or ethylenediaminetetraaceticacid (EDTA).

In some embodiments of any of the aspects, the level of expression isthe level in a sample obtained from a subject. The term “sample” or“test sample” as used herein denotes a sample taken or isolated from abiological organism, e.g., a blood or tissue sample from a subject. Insome embodiments of any of the aspects, the present inventionencompasses several examples of a biological sample. In some embodimentsof any of the aspects, the biological sample is cells, or tissue, orperipheral blood, or bodily fluid. Exemplary biological samples include,but are not limited to, a biopsy, a tumor sample, biofluid sample;blood; serum; plasma; urine; sperm; mucus; tissue biopsy; organ biopsy;synovial fluid; bile fluid; cerebrospinal fluid; mucosal secretion;effusion; sweat; saliva; and/or tissue sample etc. The term alsoincludes a mixture of the above-mentioned samples. The term “testsample” also includes untreated or pretreated (or pre-processed)biological samples. In some embodiments of any of the aspects, a testsample can comprise cells from a subject. In some embodiments of any ofthe aspects, the sample obtained from a subject can be a biopsy sample.In some embodiments of any of the aspects, the sample obtained from asubject can be a blood or serum sample.

In some embodiments of any of the aspects, the sample is anendobronchial biopsy, bronchial brushing sample, bronchial biopsy,endobronchial brushing sample, large airway biopsy, large airwaybrushing sample, nasal epithelial cells, sputum, and/or blood obtainedfrom the subject. In some embodiments of any of the aspects, the sampleis a bronchial brushing obtained from the right or left mainstembronchus. The test sample can be obtained by removing a sample from asubject, but can also be accomplished by using a previously isolatedsample (e.g. isolated at a prior timepoint and isolated by the same oranother person).

In some embodiments of any of the aspects, the test sample can be anuntreated test sample. As used herein, the phrase “untreated testsample” refers to a test sample that has not had any prior samplepre-treatment except for dilution and/or suspension in a solution.Exemplary methods for treating a test sample include, but are notlimited to, centrifugation, filtration, sonication, homogenization,heating, freezing and thawing, and combinations thereof. In someembodiments of any of the aspects, the test sample can be a frozen testsample, e.g., a frozen tissue. The frozen sample can be thawed beforeemploying methods, assays and systems described herein. After thawing, afrozen sample can be centrifuged before being subjected to methods,assays and systems described herein. In some embodiments of any of theaspects, the test sample is a clarified test sample, for example, bycentrifugation and collection of a supernatant comprising the clarifiedtest sample. In some embodiments of any of the aspects, a test samplecan be a pre-processed test sample, for example, supernatant or filtrateresulting from a treatment selected from the group consisting ofcentrifugation, filtration, thawing, purification, and any combinationsthereof. In some embodiments of any of the aspects, the test sample canbe treated with a chemical and/or biological reagent. Chemical and/orbiological reagents can be employed to protect and/or maintain thestability of the sample, including biomolecules (e.g., nucleic acid andprotein) therein, during processing. One exemplary reagent is a proteaseinhibitor, which is generally used to protect or maintain the stabilityof protein during processing. The skilled artisan is well aware ofmethods and processes appropriate for pre-processing of biologicalsamples required for determination of the level of an expression productas described herein.

In some embodiments of any of the aspects, the methods, assays, andsystems described herein can further comprise a step of obtaining orhaving obtained a test sample from a subject. In some embodiments of anyof the aspects, the subject can be a human subject. In some embodimentsof any of the aspects, the subject can be a subject in need of treatmentfor (e.g. having or diagnosed as having) premalignant lesions or asubject at risk of or at increased risk of developing bronchialpremalignant lesions as described elsewhere herein.

In some embodiments of any of the aspects, the biopsy or brushing samplecomprises morphologically-normal tissues or cells, e.g., the tissues orcells are not from a lesion and display normal morphology for their invivo location. In some embodiments of any of the aspects, the biopsy orbrushing sample consists essentially of morphologically-normal tissuesor cells. In some embodiments of any of the aspects, the biopsy orbrushing sample consists of morphologically-normal tissues or cells.

In some embodiments of any of the aspects, the biopsy or brushing samplecomprises visually-normal tissues or cells, e.g., the tissues or cellsare not from a lesion and to the unaided human eye have a normalappearance for their in vivo location. In some embodiments of any of theaspects, the biopsy or brushing sample consists essentially ofvisually-normal tissues or cells. In some embodiments of any of theaspects, the biopsy or brushing sample consists of visually-normaltissues or cells.

In some embodiments of any of the aspects, the biopsy or brushing samplecomprises bronchial premalignant lesion cells. In some embodiments ofany of the aspects, the biopsy or brushing sample consists essentiallyof bronchial premalignant lesion cells. In some embodiments of any ofthe aspects, the biopsy or brushing sample consists of bronchialpremalignant lesion cells.

A level which is less than a reference level can be a level which isless by at least about 10%, at least about 20%, at least about 50%, atleast about 60%, at least about 80%, at least about 90%, or lessrelative to the reference level. In some embodiments of any of theaspects, a level which is less than a reference level can be a levelwhich is statistically significantly less than the reference level.

A level which is more than a reference level can be a level which isgreater by at least about 10%, at least about 20%, at least about 50%,at least about 60%, at least about 80%, at least about 90%, at leastabout 100%, at least about 200%, at least about 300%, at least about500% or more than the reference level. In some embodiments of any of theaspects, a level which is more than a reference level can be a levelwhich is statistically significantly greater than the reference level.

In some embodiments of any of the aspects, the reference can be a levelof the target molecule in a population of subjects who do not have orare not diagnosed as having, and/or do not exhibit signs or symptoms ofbronchial premalignant lesions. In some embodiments of any of theaspects, the reference can also be a level of expression of the targetmolecule in a control sample, a pooled sample of control individuals ora numeric value or range of values based on the same. In someembodiments of any of the aspects, the reference can be the level of atarget molecule in a sample obtained from the same subject at an earlierpoint in time, e.g., the methods described herein can be used todetermine if a subject's sensitivity or response to a given therapy ischanging over time or if the subtype of their lesions is changing.

In some embodiments of any of the aspects, the level of expressionproducts of no more than 200 other genes is/are determined. In someembodiments of any of the aspects, the level of expression products ofno more than 100 other genes is/are determined. In some embodiments ofany of the aspects, the level of expression products of no more than 20other genes is/are determined. In some embodiments of any of theaspects, the level of expression products of no more than 10 other genesis/are determined.

In some embodiments of the foregoing aspects, the expression level of agiven gene can be normalized relative to the expression level of one ormore reference genes or reference proteins.

In some embodiments, the reference level can be the level in a sample ofsimilar cell type, sample type, sample processing, and/or obtained froma subject of similar age, sex and other demographic parameters as thesample/subject for which the level of expression is to be determined. Insome embodiments, the test sample and control reference sample are ofthe same type, that is, obtained from the same biological source, andcomprising the same composition, e.g. the same number and type of cells.

In some embodiments of any of the aspects, the reference level can be anon-proliferative reference level, e.g., the level in a tissue or cellnot comprising a proliferative lesion or from a subject who does nothave a proliferative lesion. For example, the level can be the level ininflammatory, secretory, or normal-like lesion subtypes or an average orpooling thereof.

In some embodiments, the methods described herein relate to treating asubject having or diagnosed as having bronchial premalignant lesions.Subjects having bronchial premalignant lesions can be identified by aphysician using current methods of diagnosing bronchial premalignantlesions. Tests that may aid in a diagnosis of, e.g. bronchialpremalignant lesions include, but are not limited to, bronchoscopy,autofluorescence bronchoscopy, etc. A family history of bronchialpremalignant lesions or exposure to risk factors for bronchialpremalignant lesions (e.g. cigarette smoke) can also aid in determiningif a subject is likely to have bronchial premalignant lesions or inmaking a diagnosis of bronchial premalignant lesions.

The compositions and methods described herein can be administered to asubject having or diagnosed as having bronchial premalignant lesions. Insome embodiments, the methods described herein comprise administering aneffective amount of compositions described herein to a subject in orderto alleviate a symptom of a bronchial premalignant lesions. As usedherein, “alleviating a symptom of a bronchial premalignant lesions” isameliorating any condition or symptom associated with the bronchialpremalignant lesions. As compared with an equivalent untreated control,such reduction is by at least 5%, 10%, 20%, 40%, 50%, 60%, 80%, 90%,95%, 99% or more as measured by any standard technique. A variety ofmeans for administering the compositions described herein to subjectsare known to those of skill in the art. Such methods can include, butare not limited to oral, parenteral, intravenous, intramuscular,subcutaneous, transdermal, airway (aerosol), pulmonary, cutaneous,topical, injection, or intratumoral administration. Administration canbe local or systemic.

The methods described herein can prevent, delay, or slow the developmentof lung cancer, e.g., lung squamous cell carcinoma. In some embodimentsof any of the aspects, the subject treated according to the presentmethods is not a subject with lung cancer. In some embodiments of any ofthe aspects, the subject treated according to the present methods is asubject who does not have lung cancer. In some embodiments of any of theaspects, the subject treated according to the present methods is asubject who does not have and has not had lung cancer. In someembodiments of any of the aspects, the subject treated according to thepresent methods is at risk of lung cancer. In some embodiments of any ofthe aspects, the subject is a subject with a bronchial premalignantlesion.

In some embodiments of any of the aspects, the subject is a smoker. Insome embodiments of any of the aspects, the subject is a former smoker.In some embodiments of any of the aspects, the subject is a non-smoker.

The treatments described herein, e.g. an anti-proliferative drug,anti-inflammatory drug, or immune stimulating drug can be administeredsystemically, by inhalation, and/or topically to any portion of theairways of a subject (including the nose and mouth). In some embodimentsof any of the aspects, a treatment described herein, e.g. ananti-proliferative drug, anti-inflammatory drug, or immune stimulatingdrug can be administered i) systemically and ii) by inhalation ortopically to any portion of the airways of a subject (including the noseand mouth) during a bronchoscopy or brushing collection.

An anti-proliferative drug is a drug that inhibits cell growth and/ordivision, e.g., cytostatic agents, wherein that is the primary activityof the compound in the relevant context. Non-limiting examples ofanti-proliferative drugs can include CDK inhibitors (e.g. purvalanol-a,palbociclib, ribociclib, abemaciclib, and olomoucine II); HDACinhibitors (e.g. THM-I-94, vorinostat, givinostat); PARP inhibitors(e.g. AG-14361, olaparib, rucaparib, niraparib, talazoparib, veliparib,pamiparib, CEP 9722, E7016, iniparib, 3-aminobenazmide); JAK inhibitors(e.g. JAK3-inhibitor-VI, ruxolitinib, tofacitinib, oclacitinib,baricitinib, peficitinib, filgotinib, cerdulatinib, gandotinib,lestaurtinib, momelotinib, pacritinib, PF-04965842, upadacitinib,fedratinib, cucurbitacin, CHZ868); JNK inhibitors (e.g. ZG-10,AS-601245, AM-111); MTOR inhibitors (e.g. AZD-8055, PI-103, rapamycin,temsirolimus, everolimus, ridaforolimus, rapalogs, sirolimus); FLT3inhibitors (e.g. lestaurtinib, TG-101348, gilteritinib, quizartinib,midostaurin, sorafenib, sunitinib); PI3K inhibitors (e.g. GDC-0941,PI-828, wortmannin, LY294002, hibiscone C, idelalisib, copanlisib,duvelisib, alpelisib, taselisib, perifosine, buparlisib, umbralisib,PX-866, dactolisib, CUDC-907, voxtalisib, ME-401, IPI-549, SF1126,PR6530, INK1117, pictilisib, XL147, palmoid 529, GSK1059615, ZSTK474,PWT33597, IC87114, TG100-115, CAL263, RP6503, PI-103, GNE-477,AEZS-136); AKT inhibitors (e.g. A-443644, pyrvinium-pamoate, VQD-002,perifosine, miltefosine, MK-2206, AZD5363, ipataseritib); tyrosinekinase inhibitors (e.g. aminopurvalanol-a, SU-11652, imatinib,gefitinib, erlotinib, sunitinib, adavosertib, lapatinib); protein kinaseinhibitors (e.g. HG-5-113-01, adavosertib, afatinib, axitinib,bosuntinib, cetuximab, conbimetinib, crizotinib, cabozantinib,dasatinib, entrectinib, erdafitinib, erlotinib, fostamatinib, gefitinib,ibrutinib, imatinib, lapatinib, lenvatinib, mubritinib, nilotinib,pazopanib, pegaptanib, ruxolitinib, sorafenib, sunitinib, SU6656,vandetanib, vemurafenib); RNA polymerase inhibitor (e.g. dactinomycin,triptolide); topoisomerase inhibitors (e.g. pidorubicine, doxorubicin,campothecins, indenosioquinolines, indotecan, imdimitecan, amsacrine,etoposide, teniposide, ICRF-193, genistein); HSP inhibitors (e.g.HSP90-inhibitor, 17-N-Allylamino-17-demethoxygeldanamycin (17AAG),gamitrinib); DNA protein kinase inhibitors (e.g., PIK-75); focaladhesion kinase inhibitors (e.g. PF-562271, PF573,228, PF-271, NVP-226,Y15, PND-1186, GSK2256098, VS-6062, VS-6063, VS-4718); RNA synthesisinhibitor (daunorubicin); mediator release inhibitor (e.g. ER-27319);and EZH2 inhibitors (DZNep, EPZ005687, EI1, GSK126, UNC1999, EPZ-6438,tazemetostat). Further non-limiting examples of anti-proliferative drugsinclude Acetylcholine receptor antagonists (e.g., clozapine, quetiapine,atropine, benztropine, biperiden, chlorpheniramine, citalopram,dycyclomine, dimenthydrinate, diphenhydramine, doxepin, doxylamine,glycopyrrolate, glycopyrronium, hyoscyamine, ipratropium, orphenadrine,oxitropium, oxybutynin, promethazine, propantheline bromide,scopolamine, solifenacin, solifenacin, tolterodine, tiotropium,trihexyphenidyl, tropicamide, tubocurarine, mecamylamine, hexamethonium,doxacurium, dextromethorphan, bupriopion); Acetylcholinesteraseinhibitors (e.g. Physostigmine, Neostigmine, Pyridostigmine, Ambenonium,Demecarium, Rivastigmine, Phenanthrene derivatives, Galantamine,Alpha-Pinene—noncompetitive reversible, Piperidines, Donepezil, Tacrine,Edrophonium, Huperzine A, Ladostigil, Ungeremine, Lactucopicrin, andAcotiamide); Adenosine receptor antagonists (e.g., theophylline andtheobromine); Adrenergic receptor antagonists (e.g., Phentolamine,phenoxybenzamine, Propranolol, Nebivilol, Atenolol, Oxprenolol,Metoprolol, Timolol, Pindolol, Nadolol, Pindolol, Esmolol, Acebutolol,Sotalol, Talinolol, Betaxolol, Labetalol, and Carvedilol); Angiotensinreceptor antagonists (e.g., candesartan, eprosartan, irbesartan,losartan, olmesartan, telmisartan, valsartan); Apoptosis stimulants(e.g., Asiatic acid, glycodeoxychoic acid); Cyclooxygenase inhibitors(e.g., celecoxib, rofecoxib); Cytokine production inhibitors (e.g.,sirolimus, basiliximab, daclizumab); Dehydrogenase inhibitors ((e.g.,mycophenolate-mofetil, mycophenolic acid); Dopamine receptor antagonist(e.g., benperidol, chlorpromazine, clopenthixol, droperidol,haloperidol, fluphenazine, flupenthixol, fluspirilene, penfluridol,perazine, perphenazine, pimozide, spiperone, sulpiride, thioridazine,amisulpride, aseanapine, aripriprazole, clozapine, loxapine,nemonapride, olanzapine, quetiapine, paliperidone, remoxipride,risperidone, tiapride, ziprasidone, domperidone, bromopride,metoclopramide, eticlopride, nafadotride, raclopride); EGFR inhibitors(e.g., gefitinib, erlotinib, iapatinib, osimertinib, cetuximab,neratinib, pnaitumumab, vandetanib, necitumumab, dacomitinib); ERK1 andERK2 phosphorylation inhibitors (e.g., RAF, RAS, or MEK inhibitors);Estrogen receptor agonists (e.g., ethinylestradiol, diethylstilbestrol,phytoestrogens, tamoxifen, clomifene, raloxifene); Glutamate receptorantagonists (e.g., AP5, barbiturates, dextromethorphan, dextrorphan,dizoclipin, ibogaine, ifenprodil, ketamine, kynurenic acid, memantine,perampanel, phencyclidine); Histamine receptor antagonists (e.g.,cimetidine, ranitidine, famotidine, nizatidine, roxatidine, lafutidine);Histone lysine methyltransferase inhibitors (EPZ004777, EPZ5676,BIX01294); IKK inhibitors (e.g., curcumin, embelin, auranofine, butein,IMD 0354, IKK 16, SC514, BAY 11-7082, MRT67307, BMS-345541, amlexanox,MLN120B); Ion channel antagonists (e.g., erastin); Leucine rich repeatkinase inhibitors (e.g., MLi-2, PF-06447475, GSK2578215, LRKK2-IN1, HG10/102/01, CZC-25146); MDM inhibitors (e.g., tenovin-2, idasanutlin,SP141 MI-773, R08994, AMG232, nutlin-3); Monoamine oxidase inhibitors(e.g., hydrazine, isocarboxazid, nialamide, phenelzine, hydracarbazine,tnrylcypromine, befemelane, moclobemide, pirlindole, toloxatone,rasagiline, selegiline, safinamide); nucleophosmin inhibitors (e.g.,EAPB0503, NSC348884, Rev37-47 CIGB-300, avrainvillamide, deguelin, EPTG,YTR107); PPAR receptor agonists (e.g. clofibrate, gemfibrozil,ciprofibrate, bezafibrate, fenofibrate, thiazolidinediones, BW501516,aleglitazar, muraglitizar, tesaglitzar); Phosphodiesterase inhibitors(e.g., vinpocetine, ENHA, BAY 60-7550, oxindole, PDP, IBMX,aminophylline, praxanthine, pentoxifylline, theobromine, inamrinone,milrinone, enoximone, anagrelide, cilostazol, pimobendan); SIRTinhibitors (e.g., (s)-2-phentyl-6-chloro, 8-bormo-chroman one,3′-phenethyloxy-2-anilinobenzamide); sodium channel blockers (e.g.,procainamide, quinidine, disopyramide, lidocaine, mexiletine, tocainide,phenytoin, encainide, flecainide, moricizine, propafenone); and VitaminD receptor agonists (e.g., EB 1089, BXL-01-0029, elocalcitol). In someembodiments, anti-proliferative drugs lacking anti-inflammatory activityin any context described herein can include JAK inhibitors, JNKinhibitors, AKT inhibitors, protein kinase inhibitors, RNA polymeraseinhibitors, HSP inhibitors, DNA protein kinase inhibitors, focaladhesion inhibitors, RNA synthesis inhibitors, and mediator releaseinhibitors.

As used herein, the term “anti-inflammatory” refers to a compoundcapable of reducing or inhibiting inflammation, wherein that is theprimary activity of the compound in the relevant context. As usedherein, the term “anti-inflammatory drug” or “anti-inflammatory agent”is used to describe any compound (including its analogs, derivatives,prodrugs and pharmaceutically salts) which can be used reduce or inhibitinflammation. Non-limiting examples of anti-inflammatory drugs caninclude NFkB pathway inhibitors (e.g.9-methyl-5H-6-thia-4,5-diaza-chrysene-6,6-dioxide, denosumab,disulfiram, olmesartan, dithiocarbamates, anatabine, BAY 11-7082,palmitoylethanolamide, iguartimod); protein synthesis inhibitors (e.g.chloramphenicol); anti-IL1B antibodies (e.g., Canakinumab);glucocorticoid receptor agonists (e.g. dexamethasone, mifepristone,);and TGF beta receptor inhibitors (e.g. LY-364947, GW-755.55, LY-2109761,galunisertib, SB431542, SB-525334). Further non-limiting examples ofanti-proliferative drugs include Acetylcholine receptor antagonist;Acetylcholinesterase inhibitors; Adenosine receptor antagonists;Adrenergic receptor antagonists; Angiotensin receptor antagonists;Apoptosis stimulants; Cyclooxygenase inhibitors; Cytokine productioninhibitors; Dehydrogenase inhibitors; Dopamine receptor antagonist; EGFRinhibitors; ERK1 and ERK2 phosphorylation inhibitors; Estrogen receptoragonists; Glutamate receptor antagonists; Histamine receptorantagonists; Histone lysine methyltransferase inhibitors; IKKinhibitors; Ion channel antagonists; Leucine rich repeat kinaseinhibitors; MDM inhibitors; Monoamine oxidase inhibitors; nucleophosmininhibitors; PPAR receptor agonists; Phosphodiesterase inhibitors; SIRTinhibitors; sodium channel blockers; and Vitamin D receptor agonists. Insome embodiments, anti-inflammatory drugs lacking anti-proliferativeactivity in any context described herein can include protein synthesisinhibitors and TGF beta receptor inhibitors.

It is noted herein that a single compound may exhibit multipleactivities, e.g., depending on the context. Non-examples of agents thatcan exhibit primarily an anti-inflammatory activity and/or ananti-proliferative activity, depending on the context (e.g., the subjector cell being administered/contacted with the agent) can includeAcetylcholine receptor antagonist, Acetylcholinesterase inhibitors,Adenosine receptor antagonists, Adrenergic receptor antagonists,Angiotensin receptor antagonists, Apoptosis stimulants, Aurora kinaseinhibitors, CDK inhibitors, Cyclooxygenase inhibitors, Cytokineproduction inhibitors, Dehydrogenase inhibitors, Dopamine receptorantagonist, EGFR inhibitors, ERK1 and ERK2 phosphorylation inhibitors,Estrogen receptor agonists, FLT3 inhibitors, Glucocorticoid receptoragonists, Glutamate receptor antagonists, HDAC inhibitors, Histaminereceptor antagonists, Histone lysine methyltransferase inhibitors, HSPinhibitors, IKK inhibitors, Ion channel antagonists, KIT inhibitors,Leucine rich repeat kinase inhibitors, MEK inhibitors, MDM inhibitors,Phosphodiesterase inhibitors, Monoamine oxidase inhibitors, MTORinhibitors, NFkB pathway inhibitors, nucleophosmin inhibitors, PARPinhibitors, PI3K inhibitors, PPAR receptor agonist, RAF inhibitors, SIRTinhibitors, Sodium channel blockers, Topoisomerase inhibitors, Tyrosinekinase inhibitors, VEGFR inhibitors, and a Vitamin D receptor agonists.

An immune-stimulating drug is a drug that increases the activity of theimmune system, preferably against cancer or dysplasia cells, whereinthat is the primary activity of the compound in the relevant context. Asused herein, the term “immune-stimulating drug” or “anti-inflammatoryagent” is used to describe any compound (including its analogs,derivatives, prodrugs and pharmaceutically salts) which can be usedstimulate the immune system. Non-limiting examples of immune stimulatingdrugs can include immune-checkpoint inhibitors (e.g. inhibitors against,PD-1, PD-L1, CTLA4, and LAG3); drugs that stimulate interferon signaling(e.g. anti-viral drugs that improve interferon signaling such asPegintron, Pegasys, referon A, uniferon, multiferon, rebif, avonex,cinnovex, betaseron, actimmune, reiferon, pegetron); DNA synthesisinhibitors (e.g., TAS-102, NC-6004, ganciclovir); CDK inhibitors (e.g.purvalanol-a, palbociclib, ribociclib, abemaciclib, and olomoucine II);ribonucleotide reductase inhibitors (e.g., motexafin, hydroxyurea,fludarabine, cladribine, gemcitabine, tezacitabine, triapine, galliummaltolate, gallium nitrate); dihydrofolate reductase inhibitors (e.g.,methotrexate, piritrexam, cycloguanil, JPC-2056); topoisomeraseinhibitors (e.g. pidorubicine, doxorubicin, campothecins,indenosioquinolines, indotecan, imdimitecan, amsacrine, etoposide,teniposide, ICRF-193, genistein); FLT3 inhibitors (e.g. lestaurtinib,TG-101348, gilteritinib, quizartinib, midostaurin, sorafenib,sunitinib); IGF-1 inhibitors; MEK inhibitors (e.g., trametinib,cobimetinib, binimetinib, selumetinib, PD-325901, TAK-733); aurorakinase inhibitors (e.g., ZM447439, hesperidin, VX-680); PKC inhibitors(e.g., ruboxistaurin, chelerythrine, miyabenol C, myricitrin, gossypol,verbascoside, BIM-1, bryostate 1, tamoxifen); RAF inhibitors (e.g.,vemurafenib, GDC-0879, PLX-4720, sorafenib, dabrafenib, LGX818);PDFGR/KIT inhibitors (e.g., imatinib, sunitinib, sorafenib, pazopanib,nilotinib, motesanib, linifenib); VEGFR inhibitors (e.g., axitinib,cabozantinib, lenvatinib, pazopanib, vandetanib); SRC inhibitors (e.g.,KX2-391, bosutinib, saracatinib, PP1, PP2, quercetin, dastabinib);retinoid receptor agonists (e.g., alitretinoin, isoretinoin); HDACinhibitors (e.g. THM-I-94, vorinostat, givinostat); DNAmethyltransferase inhibitors (e.g., azacytidine, decitabine,zeublarine); and EZH2 inhibitors (DZNep, EPZ005687, EI1, GSK126,UNC1999, EPZ-6438, tazemetostat).

In some embodiments, immune stimulating drugs lackinganti-proliferative/inflammatory activity in any context described hereincan include immune-checkpoint inhibitors (e.g. inhibitors against, PD-1,PD-L1, CTLA4, and LAG3); drugs that stimulate interferon signaling (e.g.anti-viral drugs that improve interferon signaling); DNA synthesisinhibitors; IMDH inhibitors; ribonucleotide reductase inhibitors;dihydrofolate reductase inhibitors; SRC inhibitors; retinoid receptoragonists; HDAC inhibitors; and DNA methyltransferase inhibitors.

The term “effective amount” as used herein refers to the amount of acomposition needed to alleviate at least one or more symptom of thedisease or disorder, and relates to a sufficient amount ofpharmacological composition to provide the desired effect. The term“therapeutically effective amount” therefore refers to an amount of thecomposition that is sufficient to provide a particular therapeuticeffect when administered to a typical subject. An effective amount asused herein, in various contexts, would also include an amountsufficient to delay the development of a symptom of the disease, alterthe course of a symptom disease (for example but not limited to, slowingthe progression of a symptom of the disease), or reverse a symptom ofthe disease. Thus, it is not generally practicable to specify an exact“effective amount”. However, for any given case, an appropriate“effective amount” can be determined by one of ordinary skill in the artusing only routine experimentation.

Effective amounts, toxicity, and therapeutic efficacy can be determinedby standard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., for determining the LD50 (the dose lethal to 50% of thepopulation) and the ED50 (the dose therapeutically effective in 50% ofthe population). The dosage can vary depending upon the dosage formemployed and the route of administration utilized. The dose ratiobetween toxic and therapeutic effects is the therapeutic index and canbe expressed as the ratio LD50/ED50. Compositions and methods thatexhibit large therapeutic indices are preferred. A therapeuticallyeffective dose can be estimated initially from cell culture assays.Also, a dose can be formulated in animal models to achieve a circulatingplasma concentration range that includes the IC50 (i.e., theconcentration of the active ingredient, which achieves a half-maximalinhibition of symptoms) as determined in cell culture, or in anappropriate animal model. Levels in plasma can be measured, for example,by high performance liquid chromatography. The effects of any particulardosage can be monitored by a suitable bioassay, e.g., assay for geneexpression as described herein, among others. The dosage can bedetermined by a physician and adjusted, as necessary, to suit observedeffects of the treatment.

In some embodiments, the technology described herein relates to apharmaceutical composition comprising a drug as described herein, andoptionally a pharmaceutically acceptable carrier. In some embodiments,the active ingredients of the pharmaceutical composition comprise thedrug as described herein. In some embodiments, the active ingredients ofthe pharmaceutical composition consist essentially of the drug asdescribed herein. In some embodiments, the active ingredients of thepharmaceutical composition consist of the drug as described herein.Pharmaceutically acceptable carriers and diluents include saline,aqueous buffer solutions, solvents and/or dispersion media. The use ofsuch carriers and diluents is well known in the art. Some non-limitingexamples of materials which can serve as pharmaceutically-acceptablecarriers include: (1) sugars, such as lactose, glucose and sucrose; (2)starches, such as corn starch and potato starch; (3) cellulose, and itsderivatives, such as sodium carboxymethyl cellulose, methylcellulose,ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4)powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, suchas magnesium stearate, sodium lauryl sulfate and talc; (8) excipients,such as cocoa butter and suppository waxes; (9) oils, such as peanutoil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil andsoybean oil; (10) glycols, such as propylene glycol; (11) polyols, suchas glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12)esters, such as ethyl oleate and ethyl laurate; (13) agar; (14)buffering agents, such as magnesium hydroxide and aluminum hydroxide;(15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18)Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21)polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents,such as polypeptides and amino acids (23) serum component, such as serumalbumin, HDL and LDL; (22) C₂-C₁₂ alcohols, such as ethanol; and (23)other non-toxic compatible substances employed in pharmaceuticalformulations. Wetting agents, coloring agents, release agents, coatingagents, sweetening agents, flavoring agents, perfuming agents,preservative and antioxidants can also be present in the formulation.The terms such as “excipient”, “carrier”, “pharmaceutically acceptablecarrier” or the like are used interchangeably herein. In someembodiments, the carrier inhibits the degradation of the active agent.

In some embodiments, the pharmaceutical composition comprising a drug asdescribed herein can be a parenteral dose form. Since administration ofparenteral dosage forms typically bypasses the patient's naturaldefenses against contaminants, parenteral dosage forms are preferablysterile or capable of being sterilized prior to administration to apatient. Examples of parenteral dosage forms include, but are notlimited to, solutions ready for injection, dry products ready to bedissolved or suspended in a pharmaceutically acceptable vehicle forinjection, suspensions ready for injection, and emulsions. In addition,controlled-release parenteral dosage forms can be prepared foradministration of a patient, including, but not limited to, DURO S®-typedosage forms and dose-dumping.

Suitable vehicles that can be used to provide parenteral dosage forms ofa drug as disclosed within are well known to those skilled in the art.Examples include, without limitation: sterile water; water for injectionUSP; saline solution; glucose solution; aqueous vehicles such as but notlimited to, sodium chloride injection, Ringer's injection, dextroseInjection, dextrose and sodium chloride injection, and lactated Ringer'sinjection; water-miscible vehicles such as, but not limited to, ethylalcohol, polyethylene glycol, and propylene glycol; and non-aqueousvehicles such as, but not limited to, corn oil, cottonseed oil, peanutoil, sesame oil, ethyl oleate, isopropyl myristate, and benzyl benzoate.Compounds that alter or modify the solubility of a pharmaceuticallyacceptable salt of the drug as disclosed herein can also be incorporatedinto the parenteral dosage forms of the disclosure, includingconventional and controlled-release parenteral dosage forms.

Pharmaceutical compositions comprising a drug can also be formulated tobe suitable for oral administration, for example as discrete dosageforms, such as, but not limited to, tablets (including withoutlimitation scored or coated tablets), pills, caplets, capsules, chewabletablets, powder packets, cachets, troches, wafers, aerosol sprays, orliquids, such as but not limited to, syrups, elixirs, solutions orsuspensions in an aqueous liquid, a non-aqueous liquid, an oil-in-wateremulsion, or a water-in-oil emulsion. Such compositions contain apredetermined amount of the pharmaceutically acceptable salt of thedisclosed compounds, and may be prepared by methods of pharmacy wellknown to those skilled in the art. See generally, Remington: The Scienceand Practice of Pharmacy, 21st Ed., Lippincott, Williams, and Wilkins,Philadelphia Pa. (2005).

Conventional dosage forms generally provide rapid or immediate drugrelease from the formulation. Depending on the pharmacology andpharmacokinetics of the drug, use of conventional dosage forms can leadto wide fluctuations in the concentrations of the drug in a patient'sblood and other tissues. These fluctuations can impact a number ofparameters, such as dose frequency, onset of action, duration ofefficacy, maintenance of therapeutic blood levels, toxicity, sideeffects, and the like. Advantageously, controlled-release formulationscan be used to control a drug's onset of action, duration of action,plasma levels within the therapeutic window, and peak blood levels. Inparticular, controlled- or extended-release dosage forms or formulationscan be used to ensure that the maximum effectiveness of a drug isachieved while minimizing potential adverse effects and safety concerns,which can occur both from under-dosing a drug (i.e., going below theminimum therapeutic levels) as well as exceeding the toxicity level forthe drug. In some embodiments, the drug can be administered in asustained release formulation.

Controlled-release pharmaceutical products have a common goal ofimproving drug therapy over that achieved by their non-controlledrelease counterparts. Ideally, the use of an optimally designedcontrolled-release preparation in medical treatment is characterized bya minimum of drug substance being employed to cure or control thecondition in a minimum amount of time. Advantages of controlled-releaseformulations include: 1) extended activity of the drug; 2) reduceddosage frequency; 3) increased patient compliance; 4) usage of lesstotal drug; 5) reduction in local or systemic side effects; 6)minimization of drug accumulation; 7) reduction in blood levelfluctuations; 8) improvement in efficacy of treatment; 9) reduction ofpotentiation or loss of drug activity; and 10) improvement in speed ofcontrol of diseases or conditions. Kim, Cherng-ju, Controlled ReleaseDosage Form Design, 2 (Technomic Publishing, Lancaster, Pa.: 2000).

Most controlled-release formulations are designed to initially releasean amount of drug (active ingredient) that promptly produces the desiredtherapeutic effect, and gradually and continually release other amountsof drug to maintain this level of therapeutic or prophylactic effectover an extended period of time. In order to maintain this constantlevel of drug in the body, the drug must be released from the dosageform at a rate that will replace the amount of drug being metabolizedand excreted from the body. Controlled-release of an active ingredientcan be stimulated by various conditions including, but not limited to,pH, ionic strength, osmotic pressure, temperature, enzymes, water, andother physiological conditions or compounds.

A variety of known controlled- or extended-release dosage forms,formulations, and devices can be adapted for use with the salts andcompositions of the disclosure. Examples include, but are not limitedto, those described in U.S. Pat. Nos. 3,845,770; 3,916,899; 3,536,809;3,598,123; 4,008,719; 5,674,533; 5,059,595; 5,591,767; 5,120,548;5,073,543; 5,639,476; 5,354,556; 5,733,566; and 6,365,185 B1; each ofwhich is incorporated herein by reference. These dosage forms can beused to provide slow or controlled-release of one or more activeingredients using, for example, hydroxypropylmethyl cellulose, otherpolymer matrices, gels, permeable membranes, osmotic systems (such asOROS® (Alza Corporation, Mountain View, Calif. USA)), or a combinationthereof to provide the desired release profile in varying proportions.

In some embodiments of any of the aspects, the drug described herein isadministered as a monotherapy, e.g., another treatment for the bronchialpremalignant lesions is not administered to the subject.

In some embodiments of any of the aspects, the methods described hereincan further comprise administering a second agent and/or treatment tothe subject, e.g. as part of a combinatorial therapy.

In certain embodiments, an effective dose of a composition comprising adrug as described herein can be administered to a patient once. Incertain embodiments, an effective dose of a composition comprising adrug can be administered to a patient repeatedly. For systemicadministration, subjects can be administered a therapeutic amount of acomposition comprising a drug, such as, e.g. 0.1 mg/kg, 0.5 mg/kg, 1.0mg/kg, 2.0 mg/kg, 2.5 mg/kg, 5 mg/kg, 10 mg/kg, 15 mg/kg, 20 mg/kg, 25mg/kg, 30 mg/kg, 40 mg/kg, 50 mg/kg, or more.

In some embodiments, after an initial treatment regimen, the treatmentscan be administered on a less frequent basis. For example, aftertreatment biweekly for three months, treatment can be repeated once permonth, for six months or a year or longer. Treatment according to themethods described herein can reduce levels of a marker or symptom of acondition, e.g. by at least 10%, at least 15%, at least 20%, at least25%, at least 30%, at least 40%, at least 50%, at least 60%, at least70%, at least 80% or at least 90% or more.

The dosage of a composition as described herein can be determined by aphysician and adjusted, as necessary, to suit observed effects of thetreatment. With respect to duration and frequency of treatment, it istypical for skilled clinicians to monitor subjects in order to determinewhen the treatment is providing therapeutic benefit, and to determinewhether to increase or decrease dosage, increase or decreaseadministration frequency, discontinue treatment, resume treatment, ormake other alterations to the treatment regimen. The dosing schedule canvary from once a week to daily depending on a number of clinicalfactors, such as the subject's sensitivity to the active ingredient. Thedesired dose or amount of activation can be administered at one time ordivided into subdoses, e.g., 2-4 subdoses and administered over a periodof time, e.g., at appropriate intervals through the day or otherappropriate schedule. In some embodiments, administration can bechronic, e.g., one or more doses and/or treatments daily over a periodof weeks or months. Examples of dosing and/or treatment schedules areadministration daily, twice daily, three times daily or four or moretimes daily over a period of 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month,2 months, 3 months, 4 months, 5 months, or 6 months, or more. Acomposition comprising a drug described herein can be administered overa period of time, such as over a 5 minute, 10 minute, 15 minute, 20minute, or 25 minute period.

The dosage ranges for the administration of a drug, according to themethods described herein depend upon, for example, the form of the drug,its potency, and the extent to which symptoms, markers, or indicators ofa condition described herein are desired to be reduced, for example thepercentage reduction desired for lesion size or the extent to which, forexample, lesion subtype changes are desired to be induced. The dosageshould not be so large as to cause adverse side effects. Generally, thedosage will vary with the age, condition, and sex of the patient and canbe determined by one of skill in the art. The dosage can also beadjusted by the individual physician in the event of any complication.

The efficacy of a drug in, e.g. the treatment of a condition describedherein, or to induce a response as described herein (e.g. reduction inlesion size) can be determined by the skilled clinician. However, atreatment is considered “effective treatment,” as the term is usedherein, if one or more of the signs or symptoms of a condition describedherein are altered in a beneficial manner, other clinically acceptedsymptoms are improved, or even ameliorated, or a desired response isinduced e.g., by at least 10% following treatment according to themethods described herein. Efficacy can be assessed, for example, bymeasuring a marker, indicator, symptom, and/or the incidence of acondition treated according to the methods described herein or any othermeasurable parameter appropriate. Efficacy can also be measured by afailure of an individual to worsen as assessed by hospitalization, orneed for medical interventions (i.e., progression of the disease ishalted). Methods of measuring these indicators are known to those ofskill in the art and/or are described herein. Treatment includes anytreatment of a disease in an individual or an animal (some non-limitingexamples include a human or an animal) and includes: (1) inhibiting thedisease, e.g., preventing a worsening of symptoms (e.g. pain orinflammation); or (2) relieving the severity of the disease, e.g.,causing regression of symptoms. An effective amount for the treatment ofa disease means that amount which, when administered to a subject inneed thereof, is sufficient to result in effective treatment as thatterm is defined herein, for that disease. Efficacy of an agent can bedetermined by assessing physical indicators of a condition or desiredresponse. It is well within the ability of one skilled in the art tomonitor efficacy of administration and/or treatment by measuring any oneof such parameters, or any combination of parameters. Efficacy can beassessed in animal models of a condition described herein, for exampletreatment of a mouse model of bronchial premalignant lesions. When usingan experimental animal model, efficacy of treatment is evidenced when astatistically significant change in a marker is observed, e.g. lesionsize or gene expression.

As used herein, “a bronchoscopy-based procedure” refers to anyendoscopic technique that permits examination of the bronchus and/orlungs. Bronchoscopy-based procedures can include white lightbronchoscopy, autofluorescence bronchoscopy, flexible bronchoscopy,rigid bronchoscopy, bronchoalveolar lavage, and the like.Bronchoscopy-based procedures can further include biopsy, brushing, ortissue sampling. If the

In addition to methods of treatment, the methods and biomarkersignatures described herein can be applied to methods of predicting therisk of lung cancer in a subject and/or determining the efficacy oftreatment or need for further treatment. For example, transition from aproliferative or inflammatory subtype to a normal-like or secretorysubtype would indicate that a treatment had been effective or that thetreatment can be discontinued.

In one aspect of any of the embodiments, described herein is a method ofpredicting the risk, or the likelihood of progression to lung cancer ina subject, the method comprising: detecting the level of expression ofat least one module 5 gene and/or at least one module 6 gene in a sampleobtained from the subject, wherein an increased level of expression ofat least one module 5 gene as compared to a non-proliferative lesionreference level; and/or a decreased level of expression of at least onemodule 6 gene as compared to a non-proliferative lesion reference levelindicates an increased risk of or likelihood of progressing to lungcancer. In one aspect of any of the embodiments, described herein is amethod of predicting the risk, or the likelihood of progression to lungcancer in a subject, the method comprising: detecting the level ofexpression of at least one module 5 gene and/or at least one module 6gene in a sample obtained from the subject at a first time point, anddetecting the level of expression of at least one module 5 gene and/orat least one module 6 gene in a sample obtained from the subject at asecond, subsequent time point, wherein an increased level of expressionof at least one module 5 gene over time; and/or a decreased level ofexpression of at least one module 6 gene over time indicates anincreased risk of or likelihood of progressing to lung cancer.

In one aspect of any of the embodiments, described herein is a method ofpredicting the risk, or the likelihood of progression to lung cancer ina subject, the method comprising: detecting the level of expression ofat least one module 9 gene and/or at least one module 10 gene in asample obtained from the subject, wherein an increased level ofexpression of at least one module 10 gene as compared to anon-proliferative lesion reference level; and/or a decreased level ofexpression of at least one module 9 gene as compared to anon-proliferative lesion reference level indicates an increased risk ofor likelihood of progressing to lung cancer. In one aspect of any of theembodiments, described herein is a method of predicting the risk, or thelikelihood of progression to lung cancer in a subject, the methodcomprising: detecting the level of expression of at least one module 10gene and/or at least one module 9 gene in a sample obtained from thesubject at a first time point, and detecting the level of expression ofat least one module 9 gene and/or at least one module 10 gene in asample obtained from the subject at a second, subsequent time point,wherein an increased level of expression of at least one module 10 geneover time; and/or a decreased level of expression of at least one module9 gene over time indicates an increased risk of or likelihood ofprogressing to lung cancer.

In one aspect of any of the embodiments, described herein is a method ofpredicting the risk, or the likelihood of progression to lung cancer ina subject, the method comprising: detecting the level of expression ofat least one module 2 gene and/or at least one module 6 gene in a sampleobtained from the subject, wherein an increased level of expression ofat least one module 2 gene as compared to a non-proliferative lesionreference level; and/or a decreased level of expression of at least onemodule 6 gene as compared to a non-proliferative lesion reference levelindicates an increased risk of or likelihood of progressing to lungcancer. In one aspect of any of the embodiments, described herein is amethod of predicting the risk, or the likelihood of progression to lungcancer in a subject, the method comprising: detecting the level ofexpression of at least one module 2 gene and/or at least one module 6gene in a sample obtained from the subject at a first time point, anddetecting the level of expression of at least one module 2 gene and/orat least one module 6 gene in a sample obtained from the subject at asecond, subsequent time point, wherein an increased level of expressionof at least one module 2 gene over time; and/or a decreased level ofexpression of at least one module 6 gene over time indicates anincreased risk of or likelihood of progressing to lung cancer.

In one aspect of any of the embodiments, described herein is a method ofdetermining treatment efficacy, the method comprising: detecting thelevel of expression of at least one module 5 gene and/or at least onemodule 6 gene in a sample obtained from the subject at a first timepoint, administering a treatment or candidate treatment, and detectingthe level of expression of at least one module 5 gene and/or at leastone module 6 gene in a sample obtained from the subject at a second,subsequent time point, wherein an decreased level of expression of atleast one module 5 gene over time; and/or an increased level ofexpression of at least one module 6 gene over time indicates thetreatment is effective.

In one aspect of any of the embodiments, described herein is a method oftreatment efficacy, the method comprising: detecting the level ofexpression of at least one module 10 gene and/or at least one module 9gene in a sample obtained from the subject at a first time point,administering a treatment or candidate treatment, and detecting thelevel of expression of at least one module 9 gene and/or at least onemodule 10 gene in a sample obtained from the subject at a second,subsequent time point, wherein an decreased level of expression of atleast one module 10 gene over time; and/or an increased level ofexpression of at least one module 9 gene over time indicates thetreatment is effective.

In one aspect of any of the embodiments, described herein is a method ofdetermining treatment efficacy, the method comprising: detecting thelevel of expression of at least one module 2 gene and/or at least onemodule 6 gene in a sample obtained from the subject at a first timepoint, administering a treatment or candidate treatment, and detectingthe level of expression of at least one module 2 gene and/or at leastone module 6 gene in a sample obtained from the subject at a second,subsequent time point, wherein an decreased level of expression of atleast one module 2 gene over time; and/or an increased level ofexpression of at least one module 6 gene over time indicates thetreatment is effective.

In one aspect of any of the embodiments, described herein is a methodcomprising: detecting the level of expression of at least one module 5gene and/or at least one module 6 gene in a sample obtained from asubject, wherein the level of expression of no more than 1,000 (e.g., nomore than 500, 400, 300, 200, or 100) genes is determined. In one aspectof any of the embodiments, described herein is a method comprising:detecting the level of expression of at least one module 9 gene and/orat least one module 10 gene in a sample obtained from a subject, whereinthe level of expression of no more than 1,000 (e.g., no more than 500,400, 300, 200, or 100) genes is determined. In one aspect of any of theembodiments, described herein is a method comprising: detecting thelevel of expression of at least one module 2 gene and/or at least onemodule 6 gene in a sample obtained from a subject, wherein the level ofexpression of no more than 1,000 (e.g., no more than 500, 400, 300, 200,or 100) genes is determined. In some embodiments of any of the aspects,the sample is a bronchial brushing sample. In some embodiments of any ofthe aspects, the at least one gene is selected from Table 14 or 15.

TABLE 13 GeneModule EnsemblID GeneSymbols 1 ENSG00000001084 GCLC 1ENSG00000006210 CX3CL1 1 ENSG00000008256 CYTH3 1 ENSG00000010319 SEMA3G1 ENSG00000011028 MRC2 1 ENSG00000011201 KAL1 1 ENSG00000011523 CEP68 1ENSG00000012660 ELOVL5 1 ENSG00000017483 SLC38A5 1 ENSG00000019144PHLDB1 1 ENSG00000019549 SNAI2 1 ENSG00000020181 GPR124 1ENSG00000020577 SAMD4A 1 ENSG00000024422 EHD2 1 ENSG00000031081 ARHGAP311 ENSG00000035862 TIMP2 1 ENSG00000042832 TG 1 ENSG00000049130 KITLG 1ENSG00000049540 ELN 1 ENSG00000050165 DKK3 1 ENSG00000053747 LAMA3 1ENSG00000054965 FAM168A 1 ENSG00000060140 STYK1 1 ENSG00000061918GUCY1B3 1 ENSG00000063180 CA11 1 ENSG00000064042 LIMCH1 1ENSG00000064205 WISP2 1 ENSG00000064300 NGFR 1 ENSG00000064989 CALCRL 1ENSG00000065054 SLC9A3R2 1 ENSG00000065320 NTN1 1 ENSG00000067445 TRO 1ENSG00000069122 GPR116 1 ENSG00000069188 SDK2 1 ENSG00000069702 TGFBR3 1ENSG00000071246 VASH1 1 ENSG00000072041 SLC6A15 1 ENSG00000072195 SPEG 1ENSG00000072210 ALDH3A2 1 ENSG00000072840 EVC 1 ENSG00000073067 CYP2W1 1ENSG00000073282 TP63 1 ENSG00000073712 FERMT2 1 ENSG00000074356 C17orf851 ENSG00000074590 NUAK1 1 ENSG00000074660 SCARF1 1 ENSG00000076706 MCAM1 ENSG00000077782 FGFR1 1 ENSG00000078018 MAP2 1 ENSG00000079102 RUNX1T11 ENSG00000079308 TNS1 1 ENSG00000080573 COL5A3 1 ENSG00000081052 COL4A41 ENSG00000081913 PHLPP1 1 ENSG00000082497 SERTAD4 1 ENSG00000082781ITGB5 1 ENSG00000085998 POMGNT1 1 ENSG00000087116 ADAMTS2 1ENSG00000087245 MMP2 1 ENSG00000088367 EPB41L1 1 ENSG00000091136 LAMB1 1ENSG00000091879 ANGPT2 1 ENSG00000092096 SLC22A17 1 ENSG00000092421SEMA6A 1 ENSG00000092969 TGFB2 1 ENSG00000099953 MMP11 1 ENSG00000100154TTC28 1 ENSG00000101331 CCM2L 1 ENSG00000101665 SMAD7 1 ENSG00000101825MXRA5 1 ENSG00000102302 FGD1 1 ENSG00000102755 FLT1 1 ENSG00000103196CRISPLD2 1 ENSG00000103241 FOXF1 1 ENSG00000103723 AP3B2 1ENSG00000103852 TTC23 1 ENSG00000104953 TLE6 1 ENSG00000105088 OLFM2 1ENSG00000105227 PRX 1 ENSG00000105371 ICAM4 1 ENSG00000105376 ICAM5 1ENSG00000105419 MEIS3 1 ENSG00000105538 RASIP1 1 ENSG00000105738 SIPA1L31 ENSG00000105866 SP4 1 ENSG00000105974 CAV1 1 ENSG00000106070 GRB10 1ENSG00000106123 EPHB6 1 ENSG00000106333 PCOLCE 1 ENSG00000106571 GLI3 1ENSG00000106624 AEBP1 1 ENSG00000108821 COL1A1 1 ENSG00000108852 MPP2 1ENSG00000108924 HLF 1 ENSG00000109099 PMP22 1 ENSG00000109107 ALDOC 1ENSG00000109193 SULT1E1 1 ENSG00000109610 SOD3 1 ENSG00000110002 VWA5A 1ENSG00000110200 ANAPC15 1 ENSG00000110799 VWF 1 ENSG00000110811 LEPREL21 ENSG00000111341 MGP 1 ENSG00000111452 GPR133 1 ENSG00000111799 COL12A11 ENSG00000112320 SOBP 1 ENSG00000112414 GPR126 1 ENSG00000112562 SMOC21 ENSG00000112769 LAMA4 1 ENSG00000112782 CLIC5 1 ENSG00000112902 SEMA5A1 ENSG00000112936 C7 1 ENSG00000112964 GHR 1 ENSG00000113140 SPARC 1ENSG00000113555 PCDH12 1 ENSG00000114270 COL7A1 1 ENSG00000114698 PLSCR41 ENSG00000114923 SLC4A3 1 ENSG00000115252 PDE1A 1 ENSG00000115306SPTBN1 1 ENSG00000115380 EFEMP1 1 ENSG00000115414 FN1 1 ENSG00000116016EPAS1 1 ENSG00000116678 LEPR 1 ENSG00000116774 OLFML3 1 ENSG00000116962NID1 1 ENSG00000117013 KCNQ4 1 ENSG00000117122 MFAP2 1 ENSG00000117385LEPRE1 1 ENSG00000117643 MAN1C1 1 ENSG00000118495 PLAGL1 1ENSG00000119138 KLF9 1 ENSG00000119681 LTBP2 1 ENSG00000119699 TGFB3 1ENSG00000119771 KLHL29 1 ENSG00000120156 TEK 1 ENSG00000120162 MOB3B 1ENSG00000120318 ARAP3 1 ENSG00000120457 KCNJ5 1 ENSG00000121068 TBX2 1ENSG00000121075 TBX4 1 ENSG00000122035 RASL11A 1 ENSG00000122642 FKBP9 1ENSG00000122707 RECK 1 ENSG00000122778 KIAA1549 1 ENSG00000122786 CALD11 ENSG00000123094 RASSF8 1 ENSG00000123384 LRP1 1 ENSG00000124006 OBSL11 ENSG00000124406 ATP8A1 1 ENSG00000125266 EFNB2 1 ENSG00000125810 CD931 ENSG00000125848 FLRT3 1 ENSG00000126803 HSPA2 1 ENSG00000127329 PTPRB1 ENSG00000127585 FBXL16 1 ENSG00000127920 GNG11 1 ENSG00000127946 HIP11 ENSG00000128052 KDR 1 ENSG00000128567 PODXL 1 ENSG00000128641 MYO1B 1ENSG00000128656 CHN1 1 ENSG00000128791 TWSG1 1 ENSG00000128872 TMOD2 1ENSG00000128917 DLL4 1 ENSG00000129009 ISLR 1 ENSG00000129038 LOXL1 1ENSG00000129467 ADCY4 1 ENSG00000129474 AJUBA 1 ENSG00000129946 SHC2 1ENSG00000129990 SYT5 1 ENSG00000130052 STARD8 1 ENSG00000130300 PLVAP 1ENSG00000130508 PXDN 1 ENSG00000130635 COL5A1 1 ENSG00000131016 AKAP12 1ENSG00000131477 RAMP2 1 ENSG00000131831 RAI2 1 ENSG00000132688 NES 1ENSG00000133026 MYH10 1 ENSG00000133067 LGR6 1 ENSG00000133110 POSTN 1ENSG00000133121 STARD13 1 ENSG00000133313 CNDP2 1 ENSG00000133687 TMTC11 ENSG00000134243 SORT1 1 ENSG00000134245 WNT2B 1 ENSG00000134318 ROCK21 ENSG00000134352 IL6ST 1 ENSG00000134569 LRP4 1 ENSG00000134590 FAM127A1 ENSG00000134627 PIWIL4 1 ENSG00000134802 SLC43A3 1 ENSG00000134853PDGFRA 1 ENSG00000134917 ADAMTS8 1 ENSG00000134986 NREP 1ENSG00000135063 FAM189A2 1 ENSG00000135111 TBX3 1 ENSG00000135423 GLS2 1ENSG00000135424 ITGA7 1 ENSG00000135775 COG2 1 ENSG00000135862 LAMC1 1ENSG00000135925 WNT10A 1 ENSG00000136114 THSD1 1 ENSG00000136158 SPRY2 1ENSG00000136160 EDNRB 1 ENSG00000136205 TNS3 1 ENSG00000136274 NACAD 1ENSG00000136546 SCN7A 1 ENSG00000137273 FOXF2 1 ENSG00000137834 SMAD6 1ENSG00000137872 SEMA6D 1 ENSG00000137962 ARHGAP29 1 ENSG00000138356 AOX11 ENSG00000138495 COX17 1 ENSG00000138735 PDE5A 1 ENSG00000138792 ENPEP1 ENSG00000138795 LEF1 1 ENSG00000139174 PRICKLE1 1 ENSG00000139211AMIGO2 1 ENSG00000139263 LRIG3 1 ENSG00000140092 FBLN5 1 ENSG00000140682TGFB1I1 1 ENSG00000140807 NKD1 1 ENSG00000140937 CDH11 1 ENSG00000141338ABCA8 1 ENSG00000141622 RNF165 1 ENSG00000141720 PIP4K2B 1ENSG00000141756 FKBP10 1 ENSG00000142156 COL6A1 1 ENSG00000142173 COL6A21 ENSG00000142798 HSPG2 1 ENSG00000143067 ZNF697 1 ENSG00000143140 GJA51 ENSG00000143341 HMCN1 1 ENSG00000143995 MEIS1 1 ENSG00000144057ST6GAL2 1 ENSG00000144642 RBMS3 1 ENSG00000144724 PTPRG 1ENSG00000144810 COL8A1 1 ENSG00000144857 BOC 1 ENSG00000145040 UCN2 1ENSG00000145147 SLIT2 1 ENSG00000145675 PIK3R1 1 ENSG00000145777 TSLP 1ENSG00000146648 EGFR 1 ENSG00000146966 DENND2A 1 ENSG00000147027 TMEM471 ENSG00000147257 GPC3 1 ENSG00000147408 CSGALNACT1 1 ENSG00000147862NFIB 1 ENSG00000148468 FAM171A1 1 ENSG00000148541 FAM13C 1ENSG00000148600 CDHR1 1 ENSG00000149212 SESN3 1 ENSG00000149294 NCAM1 1ENSG00000149485 FADS1 1 ENSG00000149564 ESAM 1 ENSG00000149575 SCN2B 1ENSG00000149582 TMEM25 1 ENSG00000149596 JPH2 1 ENSG00000149639 SOGA1 1ENSG00000150048 CLEC1A 1 ENSG00000150457 LATS2 1 ENSG00000150471 LPHN3 1ENSG00000150625 GPM6A 1 ENSG00000150938 CRIM1 1 ENSG00000151617 EDNRA 1ENSG00000151632 AKR1C2 1 ENSG00000151914 DST 1 ENSG00000152104 PTPN14 1ENSG00000152217 SETBP1 1 ENSG00000152583 SPARCL1 1 ENSG00000152990GPR125 1 ENSG00000153162 BMP6 1 ENSG00000153208 MERTK 1 ENSG00000153253SCN3A 1 ENSG00000153885 KCTD15 1 ENSG00000154065 ANKRD29 1ENSG00000154122 ANKH 1 ENSG00000154133 ROBO4 1 ENSG00000154188 ANGPT1 1ENSG00000154310 TNIK 1 ENSG00000154342 WNT3A 1 ENSG00000154358 OBSCN 1ENSG00000154767 XPC 1 ENSG00000154783 FGD5 1 ENSG00000155254 MARVELD1 1ENSG00000155324 GRAMD3 1 ENSG00000156011 PSD3 1 ENSG00000156298 TSPAN7 1ENSG00000156966 B3GNT7 1 ENSG00000157240 FZD1 1 ENSG00000157404 KIT 1ENSG00000157510 AFAP1L1 1 ENSG00000157554 ERG 1 ENSG00000158270 COLEC121 ENSG00000158301 GPRASP2 1 ENSG00000158352 SHROOM4 1 ENSG00000158435CNOT11 1 ENSG00000159164 SV2A 1 ENSG00000159640 ACE 1 ENSG00000159692CTBP1 1 ENSG00000160190 SLC37A1 1 ENSG00000160191 PDE9A 1ENSG00000160469 BRSK1 1 ENSG00000160867 FGFR4 1 ENSG00000161940 BCL6B 1ENSG00000162367 TAL1 1 ENSG00000162407 PPAP2B 1 ENSG00000162493 PDPN 1ENSG00000162552 WNT4 1 ENSG00000162576 MXRA8 1 ENSG00000162591 MEGF6 1ENSG00000162599 NFIA 1 ENSG00000162618 ELTD1 1 ENSG00000162627 SNX7 1ENSG00000162729 IGSF8 1 ENSG00000162733 DDR2 1 ENSG00000162817 C1orf1151 ENSG00000163072 NOSTRIN 1 ENSG00000163273 NPPC 1 ENSG00000163328GPR155 1 ENSG00000163359 COL6A3 1 ENSG00000163378 EOGT 1 ENSG00000163430FSTL1 1 ENSG00000163435 ELF3 1 ENSG00000163520 FBLN2 1 ENSG00000163710PCOLCE2 1 ENSG00000163827 LRRC2 1 ENSG00000164056 SPRY1 1ENSG00000164116 GUCY1A3 1 ENSG00000164176 EDIL3 1 ENSG00000164488 DACT21 ENSG00000164692 COL1A2 1 ENSG00000164741 DLC1 1 ENSG00000165125 TRPV61 ENSG00000165659 DACH1 1 ENSG00000165757 KIAA1462 1 ENSG00000165821SALL2 1 ENSG00000165995 CACNB2 1 ENSG00000166025 AMOTL1 1ENSG00000166086 JAM3 1 ENSG00000166105 GLB1L3 1 ENSG00000166147 FBN1 1ENSG00000166257 SCN3B 1 ENSG00000166265 CYYR1 1 ENSG00000166292 TMEM1001 ENSG00000166398 KIAA0355 1 ENSG00000166482 MFAP4 1 ENSG00000166813KIF7 1 ENSG00000166886 NAB2 1 ENSG00000167123 CERCAM 1 ENSG00000168056LTBP3 1 ENSG00000168060 NAALADL1 1 ENSG00000168077 SCARA3 1ENSG00000168264 IRF2BP2 1 ENSG00000168490 PHYHIP 1 ENSG00000168497 SDPR1 ENSG00000168502 SOGA2 1 ENSG00000168542 COL3A1 1 ENSG00000168621 GDNF1 ENSG00000168818 STX18 1 ENSG00000168890 TMEM150A 1 ENSG00000169047IRS1 1 ENSG00000169291 SHE 1 ENSG00000169302 STK32A 1 ENSG00000169418NPR1 1 ENSG00000169435 RASSF6 1 ENSG00000169504 CLIC4 1 ENSG00000169604ANTXR1 1 ENSG00000169744 LDB2 1 ENSG00000170017 ALCAM 1 ENSG00000170364SETMAR 1 ENSG00000170549 IRX1 1 ENSG00000170558 CDH2 1 ENSG00000170915PAQR8 1 ENSG00000171016 PYGO1 1 ENSG00000171033 PKIA 1 ENSG00000171243SOSTDC1 1 ENSG00000171346 KRT15 1 ENSG00000171444 MCC 1 ENSG00000171462DLK2 1 ENSG00000171791 BCL2 1 ENSG00000171812 COL8A2 1 ENSG00000171867PRNP 1 ENSG00000172348 RCAN2 1 ENSG00000172458 IL17D 1 ENSG00000172638EFEMP2 1 ENSG00000172889 EGFL7 1 ENSG00000173040 EVC2 1 ENSG00000173210ABLIM3 1 ENSG00000173269 MMRN2 1 ENSG00000173546 CSPG4 1 ENSG00000173706HEG1 1 ENSG00000173805 HAP1 1 ENSG00000174059 CD34 1 ENSG00000174226SNX31 1 ENSG00000174348 PODN 1 ENSG00000174370 C11orf45 1ENSG00000174567 GOLT1A 1 ENSG00000174640 SLCO2A1 1 ENSG00000175471 MCTP11 ENSG00000175920 DOK7 1 ENSG00000176393 RNPEP 1 ENSG00000176428 VPS37D1 ENSG00000176435 CLEC14A 1 ENSG00000176771 NCKAP5 1 ENSG00000176971FIBIN 1 ENSG00000177076 ACER2 1 ENSG00000177303 CASKIN2 1ENSG00000177469 PTRF 1 ENSG00000177707 PVRL3 1 ENSG00000177732 SOX12 1ENSG00000178031 ADAMTSL1 1 ENSG00000178222 RNF212 1 ENSG00000178947LINC00086 1 ENSG00000179104 TMTC2 1 ENSG00000179348 GATA2 1ENSG00000179431 FJX1 1 ENSG00000179776 CDH5 1 ENSG00000180739 S1PR5 1ENSG00000180875 GREM2 1 ENSG00000181104 F2R 1 ENSG00000182175 RGMA 1ENSG00000182272 B4GALNT4 1 ENSG00000182492 BGN 1 ENSG00000182534 MXRA7 1ENSG00000182621 PLCB1 1 ENSG00000182871 COL18A1 1 ENSG00000182985 CADM11 ENSG00000183087 GAS6 1 ENSG00000183160 TMEM119 1 ENSG00000183722 LHFP1 ENSG00000183729 NPBWR1 1 ENSG00000183734 ASCL2 1 ENSG00000183853KIRREL 1 ENSG00000183963 SMTN 1 ENSG00000184113 CLDN5 1 ENSG00000184564SLITRK6 1 ENSG00000184916 JAG2 1 ENSG00000184985 SORCS2 1ENSG00000185070 FLRT2 1 ENSG00000185418 TARSL2 1 ENSG00000185652 NTF3 1ENSG00000185668 POU3F1 1 ENSG00000185924 RTN4RL1 1 ENSG00000186260 MKL21 ENSG00000186318 BACE1 1 ENSG00000186462 NAP1L2 1 ENSG00000186732MPPED1 1 ENSG00000186994 KANK3 1 ENSG00000186998 EMID1 1 ENSG00000187068C3orf70 1 ENSG00000187134 AKR1C1 1 ENSG00000187193 MT1X 1ENSG00000187244 BCAM 1 ENSG00000187513 GJA4 1 ENSG00000187678 SPRY4 1ENSG00000187720 THSD4 1 ENSG00000187955 COL14A1 1 ENSG00000188153 COL4A51 ENSG00000188677 PARVB 1 ENSG00000189376 C8orf76 1 ENSG00000196139AKR1C3 1 ENSG00000196569 LAMA2 1 ENSG00000197256 KANK2 1 ENSG00000197321SVIL 1 ENSG00000197380 DACT3 1 ENSG00000197461 PDGFA 1 ENSG00000197467COL13A1 1 ENSG00000197496 SLC2A10 1 ENSG00000197565 COL4A6 1ENSG00000197614 MFAP5 1 ENSG00000197696 NMB 1 ENSG00000198300 PEG3 1ENSG00000198719 DLL1 1 ENSG00000198728 LDB1 1 ENSG00000198835 GJC2 1ENSG00000198853 RUSC2 1 ENSG00000198873 GRK5 1 ENSG00000198885 ITPRIPL11 ENSG00000204175 GPRIN2 1 ENSG00000204262 COL5A2 1 ENSG00000204301NOTCH4 1 ENSG00000205795 CYS1 1 ENSG00000211450 C11orf31 1ENSG00000212747 FAM127C 1 ENSG00000213689 TREX1 1 ENSG00000213903 LTB4R1 ENSG00000214860 EVPLL 1 ENSG00000215218 UBE2QL1 1 ENSG00000221866PLXNA4 1 ENSG00000221968 FADS3 1 ENSG00000224652 LINC00885 1ENSG00000225950 NTF4 1 ENSG00000229852 1 ENSG00000230937 MIR205HG 1ENSG00000231789 1 ENSG00000239911 PRKAG2-AS1 1 ENSG00000240583 AQP1 1ENSG00000240771 ARHGEF25 1 ENSG00000241127 YAE1D1 1 ENSG00000241644 INMT1 ENSG00000243244 STON1 1 ENSG00000250685 1 ENSG00000251322 SHANK3 1ENSG00000256309 1 ENSG00000257026 1 ENSG00000269113 TRABD2B 1ENSG00000269190 FBXO17 1 ENSG00000269905 1 ENSG00000272327 1ENSG00000272734 ADIRF-AS1 2 ENSG00000001631 KRIT1 2 ENSG00000002016RAD52 2 ENSG00000003756 RBM5 2 ENSG00000004534 RBM6 2 ENSG00000004777ARHGAP33 2 ENSG00000006025 OSBPL7 2 ENSG00000006194 ZNF263 2ENSG00000006530 AGK 2 ENSG00000007392 LUC7L 2 ENSG00000008128 CDK11A 2ENSG00000009724 MASP2 2 ENSG00000011021 CLCN6 2 ENSG00000011243 AKAP8L 2ENSG00000011376 LARS2 2 ENSG00000013441 CLK1 2 ENSG00000013561 RNF14 2ENSG00000018189 RUFY3 2 ENSG00000028310 BRD9 2 ENSG00000032219 ARID4A 2ENSG00000033030 ZCCHC8 2 ENSG00000038358 EDC4 2 ENSG00000044446 PHKA2 2ENSG00000047634 SCML1 2 ENSG00000051009 FAM160A2 2 ENSG00000053438 NNAT2 ENSG00000055955 ITIH4 2 ENSG00000056558 TRAF1 2 ENSG00000058673ZC3H11A 2 ENSG00000059588 TARBP1 2 ENSG00000061936 SFSWAP 2ENSG00000061987 MON2 2 ENSG00000064607 SUGP2 2 ENSG00000064687 ABCA7 2ENSG00000067191 CACNB1 2 ENSG00000068697 LAPTM4A 2 ENSG00000068745 IP6K22 ENSG00000069493 CLEC2D 2 ENSG00000070476 ZXDC 2 ENSG00000070610 GBA2 2ENSG00000070669 ASNS 2 ENSG00000073605 GSDMB 2 ENSG00000074582 BCS1L 2ENSG00000074696 PTPLAD1 2 ENSG00000075413 MARK3 2 ENSG00000075826 SEC31B2 ENSG00000077458 FAM76B 2 ENSG00000078403 MLLT10 2 ENSG00000079134THOC1 2 ENSG00000081019 RSBN1 2 ENSG00000081665 ZNF506 2 ENSG00000081791KIAA0141 2 ENSG00000082258 CCNT2 2 ENSG00000084463 WBP11 2ENSG00000085465 OVGP1 2 ENSG00000087087 SRRT 2 ENSG00000087157 PGS1 2ENSG00000088038 CNOT3 2 ENSG00000088448 ANKRD10 2 ENSG00000089280 FUS 2ENSG00000090432 MUL1 2 ENSG00000090905 TNRC6A 2 ENSG00000092094 OSGEP 2ENSG00000092529 CAPN3 2 ENSG00000094631 HDAC6 2 ENSG00000094914 AAAS 2ENSG00000095066 HOOK2 2 ENSG00000095564 BTAF1 2 ENSG00000099251HSD17B7P2 2 ENSG00000099940 SNAP29 2 ENSG00000099949 LZTR1 2ENSG00000100038 TOP3B 2 ENSG00000100068 LRP5L 2 ENSG00000100197 CYP2D6 2ENSG00000100201 DDX17 2 ENSG00000100288 CHKB 2 ENSG00000100416 TRMU 2ENSG00000100445 SDR39U1 2 ENSG00000100483 VCPKMT 2 ENSG00000100650 SRSF52 ENSG00000100726 TELO2 2 ENSG00000100813 ACIN1 2 ENSG00000100836 PABPN12 ENSG00000100941 PNN 2 ENSG00000101049 SGK2 2 ENSG00000101104 PABPC1L 2ENSG00000101901 ALG13 2 ENSG00000102057 KCND1 2 ENSG00000102125 TAZ 2ENSG00000102287 GABRE 2 ENSG00000102878 HSF4 2 ENSG00000102901 CENPT 2ENSG00000102908 NFAT5 2 ENSG00000103091 WDR59 2 ENSG00000103168 TAF1C 2ENSG00000104365 IKBKB 2 ENSG00000104852 SNRNP70 2 ENSG00000104957CCDC130 2 ENSG00000105127 AKAP8 2 ENSG00000105136 ZNF419 2ENSG00000105612 DNASE2 2 ENSG00000105875 WDR91 2 ENSG00000106133 NSUN5P22 ENSG00000106344 RBM28 2 ENSG00000106608 URGCP 2 ENSG00000106635 BCL7B2 ENSG00000108100 CCNY 2 ENSG00000108296 CWC25 2 ENSG00000108389 MTMR4 2ENSG00000108465 CDK5RAP3 2 ENSG00000108474 PIGL 2 ENSG00000108654 DDX5 2ENSG00000108773 KAT2A 2 ENSG00000108799 EZH1 2 ENSG00000108848 LUC7L3 2ENSG00000108963 DPH1 2 ENSG00000109046 WSB1 2 ENSG00000109063 MYH3 2ENSG00000109920 FNBP4 2 ENSG00000110066 SUV420H1 2 ENSG00000110455 ACCS2 ENSG00000110721 CHKA 2 ENSG00000110888 CAPRIN2 2 ENSG00000111011 RSRC22 ENSG00000111203 ITFG2 2 ENSG00000111231 GPN3 2 ENSG00000111271 ACAD102 ENSG00000111364 DDX55 2 ENSG00000111664 GNB3 2 ENSG00000111785 RIC8B 2ENSG00000111788 2 ENSG00000112309 B3GAT2 2 ENSG00000112357 PEX7 2ENSG00000112983 BRD8 2 ENSG00000113108 APBB3 2 ENSG00000113240 CLK4 2ENSG00000113649 TCERG1 2 ENSG00000113971 NPHP3 2 ENSG00000114742 WDR48 2ENSG00000114770 ABCC5 2 ENSG00000114857 NKTR 2 ENSG00000114982 KANSL3 2ENSG00000115234 SNX17 2 ENSG00000115282 TTC31 2 ENSG00000115459 ELMOD3 2ENSG00000115524 SF3B1 2 ENSG00000115875 SRSF7 2 ENSG00000116001 TIA1 2ENSG00000116350 SRSF4 2 ENSG00000116497 S100PBP 2 ENSG00000116560 SFPQ 2ENSG00000116580 GON4L 2 ENSG00000116584 ARHGEF2 2 ENSG00000116754 SRSF112 ENSG00000116883 2 ENSG00000117360 PRPF3 2 ENSG00000117569 PTBP2 2ENSG00000117616 C1orf63 2 ENSG00000117862 TXNDC12 2 ENSG00000118482 PHF32 ENSG00000118557 PMFBP1 2 ENSG00000119707 RBM25 2 ENSG00000119906FAM178A 2 ENSG00000120049 KCNIP2 2 ENSG00000120458 MSANTD2 2ENSG00000120662 MTRF1 2 ENSG00000120798 NR2C1 2 ENSG00000120832 MTERFD32 ENSG00000121274 PAPD5 2 ENSG00000121310 ECHDC2 2 ENSG00000121454 LHX42 ENSG00000121716 PILRB 2 ENSG00000122085 MTERFD2 2 ENSG00000122257RBBP6 2 ENSG00000122678 POLM 2 ENSG00000122965 RBM19 2 ENSG00000124098FAM210B 2 ENSG00000124160 NCOA5 2 ENSG00000124193 SRSF6 2ENSG00000124222 STX16 2 ENSG00000124593 PRICKLE4 2 ENSG00000124743KLHL31 2 ENSG00000125447 GGA3 2 ENSG00000125633 CCDC93 2 ENSG00000125814NAPB 2 ENSG00000125818 PSMF1 2 ENSG00000125846 ZNF133 2 ENSG00000126070AGO3 2 ENSG00000126217 MCF2L 2 ENSG00000126453 BCL2L12 2 ENSG00000126456IRF3 2 ENSG00000126500 FLRT1 2 ENSG00000126746 ZNF384 2 ENSG00000126775ATG14 2 ENSG00000127366 TAS2R5 2 ENSG00000127586 CHTF18 2ENSG00000127957 PMS2P3 2 ENSG00000128000 ZNF780B 2 ENSG00000128159TUBGCP6 2 ENSG00000128563 PRKRIP1 2 ENSG00000128699 ORMDL1 2ENSG00000128915 NARG2 2 ENSG00000129055 ANAPC13 2 ENSG00000129351 ILF3 2ENSG00000129472 RAB2B 2 ENSG00000129484 PARP2 2 ENSG00000129933 MAU2 2ENSG00000130254 SAFB2 2 ENSG00000130653 PNPLA7 2 ENSG00000130684 ZNF3372 ENSG00000130948 HSD17B3 2 ENSG00000131051 RBM39 2 ENSG00000131127ZNF141 2 ENSG00000131398 KCNC3 2 ENSG00000131591 C1orf159 2ENSG00000131797 CLUHP3 2 ENSG00000132424 PNISR 2 ENSG00000132485 ZRANB22 ENSG00000132680 KIAA0907 2 ENSG00000132780 NASP 2 ENSG00000132793LPIN3 2 ENSG00000132952 USPL1 2 ENSG00000133318 RTN3 2 ENSG00000133466C1QTNF6 2 ENSG00000133619 KRBA1 2 ENSG00000133624 ZNF767 2ENSG00000133858 ZFC3H1 2 ENSG00000134186 PRPF38B 2 ENSG00000134253TRIM45 2 ENSG00000134453 RBM17 2 ENSG00000134744 ZCCHC11 2ENSG00000134884 ARGLU1 2 ENSG00000135164 DMTF1 2 ENSG00000135407 AVIL 2ENSG00000135437 RDH5 2 ENSG00000135473 PAN2 2 ENSG00000135637 CCDC142 2ENSG00000135740 SLC9A5 2 ENSG00000135976 ANKRD36 2 ENSG00000136271 DDX562 ENSG00000136819 C9orf78 2 ENSG00000137185 ZSCAN9 2 ENSG00000137343ATAT1 2 ENSG00000137504 CREBZF 2 ENSG00000137776 SLTM 2 ENSG00000137802MAPKBP1 2 ENSG00000137817 PARP6 2 ENSG00000137822 TUBGCP4 2ENSG00000138050 THUMPD2 2 ENSG00000138109 CYP2C9 2 ENSG00000138658C4orf21 2 ENSG00000138834 MAPK8IP3 2 ENSG00000139190 VAMP1 2ENSG00000139574 NPFF 2 ENSG00000139631 CSAD 2 ENSG00000139746 RBM26 2ENSG00000139908 TSSK4 2 ENSG00000140009 ESR2 2 ENSG00000140181 HERC2P2 2ENSG00000140398 NEIL1 2 ENSG00000140400 MAN2C1 2 ENSG00000140474 ULK3 2ENSG00000140488 CELF6 2 ENSG00000140983 RHOT2 2 ENSG00000141068 KSR1 2ENSG00000141258 SGSM2 2 ENSG00000141551 CSNK1D 2 ENSG00000141564 RPTOR 2ENSG00000142102 ATHL1 2 ENSG00000142166 IFNAR1 2 ENSG00000142233 NTN5 2ENSG00000143178 TBX19 2 ENSG00000143183 TMCO1 2 ENSG00000143190 POU2F1 2ENSG00000143379 SETDB1 2 ENSG00000143434 SEMA6C 2 ENSG00000143442 POGZ 2ENSG00000143630 HCN3 2 ENSG00000144026 ZNF514 2 ENSG00000144161 ZC3H8 2ENSG00000144524 COPS7B 2 ENSG00000145020 AMT 2 ENSG00000145029 NICN1 2ENSG00000145908 ZNF300 2 ENSG00000146021 KLHL3 2 ENSG00000146067 FAM193B2 ENSG00000146215 CRIP3 2 ENSG00000146556 WASH2P 2 ENSG00000146826C7orf43 2 ENSG00000146830 GIGYF1 2 ENSG00000146963 C7orf55- LUC7L2 2ENSG00000147118 ZNF182 2 ENSG00000147121 KRBOX4 2 ENSG00000147162 OGT 2ENSG00000147174 ACRC 2 ENSG00000147180 ZNF711 2 ENSG00000147437 GNRH1 2ENSG00000147576 ADHFE1 2 ENSG00000147789 ZNF7 2 ENSG00000147854 UHRF2 2ENSG00000148200 NR6A1 2 ENSG00000148399 DPH7 2 ENSG00000149532 CPSF7 2ENSG00000151006 PRSS53 2 ENSG00000151303 AGAP11 2 ENSG00000151376 ME3 2ENSG00000151849 CENPJ 2 ENSG00000152042 NBPF11 2 ENSG00000152117 2ENSG00000152433 ZNF547 2 ENSG00000152520 PAN3 2 ENSG00000152527 PLEKHH22 ENSG00000152795 HNRNPDL 2 ENSG00000152926 ZNF117 2 ENSG00000153291SLC25A27 2 ENSG00000153666 GOLGA8I 2 ENSG00000153914 SREK1 2ENSG00000154144 TBRG1 2 ENSG00000154263 ABCA10 2 ENSG00000154832 CXXC1 2ENSG00000155229 MMS19 2 ENSG00000155256 ZFYVE27 2 ENSG00000155657 TTN 2ENSG00000155903 RASA2 2 ENSG00000156639 ZFAND3 2 ENSG00000156642 NPTN 2ENSG00000157306 2 ENSG00000157741 UBN2 2 ENSG00000157764 BRAF 2ENSG00000158286 RNF207 2 ENSG00000158805 ZNF276 2 ENSG00000158815 FGF172 ENSG00000159086 PAXBP1 2 ENSG00000159140 SON 2 ENSG00000159346 ADIPOR12 ENSG00000159461 AMFR 2 ENSG00000160072 ATAD3B 2 ENSG00000160323ADAMTS13 2 ENSG00000160781 PAQR6 2 ENSG00000160828 STAG3L2 2ENSG00000160953 MUM1 2 ENSG00000160961 ZNF333 2 ENSG00000161265 U2AF1L42 ENSG00000161547 SRSF2 2 ENSG00000161664 ASB16 2 ENSG00000161912ADCY10P1 2 ENSG00000162086 ZNF75A 2 ENSG00000162231 NXF1 2ENSG00000162408 NOL9 2 ENSG00000162461 SLC25A34 2 ENSG00000162526 TSSK32 ENSG00000162572 SCNN1D 2 ENSG00000162601 MYSM1 2 ENSG00000162650ATXN7L2 2 ENSG00000162735 PEX19 2 ENSG00000162997 PRORSD1P 2ENSG00000163354 DCST2 2 ENSG00000163660 CCNL1 2 ENSG00000163714 U2SURP 2ENSG00000163728 TTC14 2 ENSG00000163867 ZMYM6 2 ENSG00000163945 UVSSA 2ENSG00000164048 ZNF589 2 ENSG00000164073 MFSD8 2 ENSG00000164074 C4orf292 ENSG00000164241 C5orf63 2 ENSG00000164406 LEAP2 2 ENSG00000164548TRA2A 2 ENSG00000164877 MICALL2 2 ENSG00000164879 CA3 2 ENSG00000165275TRMT10B 2 ENSG00000165494 PCF11 2 ENSG00000165699 TSC1 2 ENSG00000165792METTL17 2 ENSG00000165819 METTL3 2 ENSG00000166012 TAF1D 2ENSG00000166169 POLL 2 ENSG00000166261 ZNF202 2 ENSG00000166321 NUDT13 2ENSG00000166343 MSS51 2 ENSG00000166405 RIC3 2 ENSG00000166432 ZMAT1 2ENSG00000166436 TRIM66 2 ENSG00000166667 SPDYE6 2 ENSG00000166762CATSPER2 2 ENSG00000166801 FAM111A 2 ENSG00000166887 VPS39 2ENSG00000167280 ENGASE 2 ENSG00000167302 ENTHD2 2 ENSG00000167371 PRRT22 ENSG00000167380 ZNF226 2 ENSG00000167524 2 ENSG00000167549 CORO6 2ENSG00000167566 NCKAP5L 2 ENSG00000167615 LENG8 2 ENSG00000167674 2ENSG00000167702 KIFC2 2 ENSG00000167766 ZNF83 2 ENSG00000167978 SRRM2 2ENSG00000168005 C11orf84 2 ENSG00000168010 ATG16L2 2 ENSG00000168066 SF12 ENSG00000168096 ANKS3 2 ENSG00000168137 SETD5 2 ENSG00000168310 IRF2 2ENSG00000168395 ING5 2 ENSG00000168566 SNRNP48 2 ENSG00000168614 NBPF9 2ENSG00000168876 ANKRD49 2 ENSG00000168887 C2orf68 2 ENSG00000168939SPRY3 2 ENSG00000168970 JMJD7- PLA2G4B 2 ENSG00000169045 HNRNPH1 2ENSG00000169131 ZNF354A 2 ENSG00000169203 2 ENSG00000169246 NPIPB3 2ENSG00000169592 INO80E 2 ENSG00000169660 HEXDC 2 ENSG00000169885 CALML62 ENSG00000169914 OTUD3 2 ENSG00000170049 KCNAB3 2 ENSG00000170074FAM153A 2 ENSG00000170234 PWWP2A 2 ENSG00000170581 STAT2 2ENSG00000170919 TPT1-AS1 2 ENSG00000170949 ZNF160 2 ENSG00000171163ZNF692 2 ENSG00000171456 ASXL1 2 ENSG00000171824 EXOSC10 2ENSG00000172273 HINFP 2 ENSG00000172345 STARD5 2 ENSG00000172354 GNB2 2ENSG00000172650 AGAP5 2 ENSG00000172732 MUS81 2 ENSG00000172803 SNX32 2ENSG00000172890 NADSYN1 2 ENSG00000173064 HECTD4 2 ENSG00000173209 AHSA22 ENSG00000173275 ZNF449 2 ENSG00000173531 MST1 2 ENSG00000173575 CHD2 2ENSG00000173681 CXorf23 2 ENSG00000173991 TCAP 2 ENSG00000174093 2ENSG00000174194 AGAP8 2 ENSG00000174353 STAG3L3 2 ENSG00000174652 ZNF2662 ENSG00000175066 GK5 2 ENSG00000175265 GOLGA8A 2 ENSG00000175309 PHYKPL2 ENSG00000175322 ZNF519 2 ENSG00000175455 CCDC14 2 ENSG00000175787ZNF169 2 ENSG00000176444 CLK2 2 ENSG00000176681 LRRC37A 2ENSG00000176946 THAP4 2 ENSG00000177042 TMEM80 2 ENSG00000177202 SPACA42 ENSG00000177225 PDDC1 2 ENSG00000177479 ARIH2 2 ENSG00000177485 ZBTB332 ENSG00000177595 PIDD 2 ENSG00000177853 ZNF518A 2 ENSG00000177943MAMDC4 2 ENSG00000178028 DMAP1 2 ENSG00000178038 ALS2CL 2ENSG00000178188 SH2B1 2 ENSG00000178252 WDR6 2 ENSG00000178338 ZNF354B 2ENSG00000178397 FAM220A 2 ENSG00000178567 EPM2AIP1 2 ENSG00000178761FAM219B 2 ENSG00000179304 FAM156B 2 ENSG00000179406 LINC00174 2ENSG00000179979 CRIPAK 2 ENSG00000180113 TDRD6 2 ENSG00000180855 ZNF4432 ENSG00000180902 D2HGDH 2 ENSG00000181045 SLC26A11 2 ENSG00000181523SGSH 2 ENSG00000181852 RNF41 2 ENSG00000182230 FAM153B 2 ENSG00000182308DCAF4L1 2 ENSG00000182310 SPACA6P 2 ENSG00000182324 KCNJ14 2ENSG00000182378 PLCXD1 2 ENSG00000182473 EXOC7 2 ENSG00000182484 WASH6P2 ENSG00000182646 FAM156A 2 ENSG00000182685 BRICD5 2 ENSG00000182796TMEM198B 2 ENSG00000182841 RRP7B 2 ENSG00000182873 2 ENSG00000182944EWSR1 2 ENSG00000182983 ZNF662 2 ENSG00000182986 ZNF320 2ENSG00000183281 PLGLB1 2 ENSG00000183291 2 ENSG00000183423 LRIT3 2ENSG00000183718 TRIM52 2 ENSG00000184343 SRPK3 2 ENSG00000184402 SS18L12 ENSG00000184441 2 ENSG00000184465 WDR27 2 ENSG00000184634 MED12 2ENSG00000184640 9-Sep 2 ENSG00000184677 ZBTB40 2 ENSG00000184787 UBE2G22 ENSG00000184863 RBM33 2 ENSG00000184925 LCN12 2 ENSG00000185101 ANO9 2ENSG00000185122 HSF1 2 ENSG00000185128 TBC1D3F 2 ENSG00000185189 NRBP2 2ENSG00000185219 ZNF445 2 ENSG00000185246 PRPF39 2 ENSG00000185324 CDK102 ENSG00000185485 SDHAP1 2 ENSG00000185596 WASH3P 2 ENSG00000185684EP400NL 2 ENSG00000185829 ARL17A 2 ENSG00000185842 DNAH14 2ENSG00000185864 NPIPB4 2 ENSG00000185946 RNPC3 2 ENSG00000185986 SDHAP32 ENSG00000186088 GSAP 2 ENSG00000186166 CCDC84 2 ENSG00000186204CYP4F12 2 ENSG00000186275 NBPF12 2 ENSG00000186283 TOR3A 2ENSG00000186301 MST1P2 2 ENSG00000186376 ZNF75D 2 ENSG00000186566GPATCH8 2 ENSG00000186567 CEACAM19 2 ENSG00000186715 MST1L 2ENSG00000186812 ZNF397 2 ENSG00000186814 ZSCAN30 2 ENSG00000186834HEXIM1 2 ENSG00000186908 ZDHHC17 2 ENSG00000187066 TMEM262 2ENSG00000187961 KLHL17 2 ENSG00000188206 HNRNPU-AS1 2 ENSG00000188227ZNF793 2 ENSG00000188234 AGAP4 2 ENSG00000188428 BLOC1S5 2ENSG00000188529 SRSF10 2 ENSG00000188554 NBR1 2 ENSG00000188738 FSIP2 2ENSG00000188811 NHLRC3 2 ENSG00000188827 SLX4 2 ENSG00000189007 ADAT2 2ENSG00000189136 UBE2Q2P1 2 ENSG00000196074 SYCP2 2 ENSG00000196123KIAA0895L 2 ENSG00000196295 2 ENSG00000196296 ATP2A1 2 ENSG00000196387ZNF140 2 ENSG00000196409 ZNF658 2 ENSG00000196440 ARMCX4 2ENSG00000196644 GPR89C 2 ENSG00000196648 GOLGA6L20 2 ENSG00000196670ZFP62 2 ENSG00000196689 TRPV1 2 ENSG00000196696 PDXDC2P 2ENSG00000196757 ZNF700 2 ENSG00000196912 ANKRD36B 2 ENSG00000197119SLC25A29 2 ENSG00000197124 ZNF682 2 ENSG00000197162 ZNF785 2ENSG00000197182 2 ENSG00000197343 ZNF655 2 ENSG00000197558 SSPO 2ENSG00000197608 ZNF841 2 ENSG00000197681 TBC1D3 2 ENSG00000197774 EME2 2ENSG00000197857 ZNF44 2 ENSG00000197948 FCHSD1 2 ENSG00000197961 ZNF1212 ENSG00000197976 AKAP17A 2 ENSG00000197989 SNHG12 2 ENSG00000198035AGAP9 2 ENSG00000198040 ZNF84 2 ENSG00000198064 2 ENSG00000198105 ZNF2482 ENSG00000198150 2 ENSG00000198198 SZT2 2 ENSG00000198231 DDX42 2ENSG00000198276 UCKL1 2 ENSG00000198393 ZNF26 2 ENSG00000198556 ZNF789 2ENSG00000198563 DDX39B 2 ENSG00000198590 C3orf35 2 ENSG00000198625 MDM42 ENSG00000198799 LRIG2 2 ENSG00000203392 2 ENSG00000203667 COX20 2ENSG00000203709 C1orf132 2 ENSG00000203761 MSTO2P 2 ENSG00000203815FAM231D 2 ENSG00000203880 PCMTD2 2 ENSG00000204149 AGAP6 2ENSG00000204164 BMS1P5 2 ENSG00000204271 SPIN3 2 ENSG00000204305 AGER 2ENSG00000204311 DFNB59 2 ENSG00000204348 DXO 2 ENSG00000204351 SKIV2L 2ENSG00000204410 MSH5 2 ENSG00000204514 ZNF814 2 ENSG00000204576 PRR3 2ENSG00000204681 GABBR1 2 ENSG00000204946 ZNF783 2 ENSG00000205047 2ENSG00000205085 FAM71F2 2 ENSG00000205238 SPDYE2 2 ENSG00000205307 SAP252 ENSG00000205560 CPT1B 2 ENSG00000205583 STAG3L1 2 ENSG00000205885C1RL-AS1 2 ENSG00000205890 2 ENSG00000205923 CEMP1 2 ENSG00000205959 2ENSG00000206149 HERC2P9 2 ENSG00000206417 H1FX-AS1 2 ENSG00000206573SETD5-AS1 2 ENSG00000211454 AKR7L 2 ENSG00000212123 PRR22 2ENSG00000212127 TAS2R14 2 ENSG00000212694 2 ENSG00000213139 CRYGS 2ENSG00000213190 MLLT11 2 ENSG00000213246 SUPT4H1 2 ENSG00000213339 QTRT12 ENSG00000213347 MXD3 2 ENSG00000213443 2 ENSG00000213599 SLX1A-SULT1A3 2 ENSG00000213901 SLC23A3 2 ENSG00000213918 DNASE1 2ENSG00000213983 AP1G2 2 ENSG00000213999 MEF2B 2 ENSG00000214021 TTLL3 2ENSG00000214135 2 ENSG00000214176 PLEKHM1P 2 ENSG00000214279 2ENSG00000214331 2 ENSG00000214455 RCN1P2 2 ENSG00000214756 METTL12 2ENSG00000214765 SEPT7P2 2 ENSG00000214783 POLR2J4 2 ENSG00000214826DDX12P 2 ENSG00000214827 MTCP1 2 ENSG00000215022 2 ENSG00000215041NEURL4 2 ENSG00000215126 CBWD7 2 ENSG00000215158 2 ENSG00000215252GOLGA8B 2 ENSG00000215298 2 ENSG00000215375 MYL5 2 ENSG00000215417MIR17HG 2 ENSG00000215424 MCM3AP- AS1 2 ENSG00000215440 NPEPL1 2ENSG00000215513 PI4KAP1 2 ENSG00000215769 2 ENSG00000215788 TNFRSF25 2ENSG00000216937 CCDC7 2 ENSG00000218891 ZNF579 2 ENSG00000220201 ZGLP1 2ENSG00000221944 TIGD1 2 ENSG00000221978 CCNL2 2 ENSG00000223509 2ENSG00000223705 NSUN5P1 2 ENSG00000223745 2 ENSG00000223839 FAM95B1 2ENSG00000223959 AFG3L1P 2 ENSG00000224186 C5orf66 2 ENSG00000224660SH3BP5-AS1 2 ENSG00000224956 2 ENSG00000224975 INE1 2 ENSG00000225032 2ENSG00000225138 2 ENSG00000225313 2 ENSG00000225373 WASH5P 2ENSG00000225697 SLC26A6 2 ENSG00000225828 FAM229A 2 ENSG00000225855RUSC1-AS1 2 ENSG00000225892 2 ENSG00000226232 2 ENSG00000226332 2ENSG00000226696 LENG8-AS1 2 ENSG00000226763 SRRM5 2 ENSG00000227232WASH7P 2 ENSG00000227543 SPAG5-AS1 2 ENSG00000227671 MIR3916 2ENSG00000227896 2 ENSG00000228274 2 ENSG00000228315 GUSBP11 2ENSG00000228393 LINC01004 2 ENSG00000228409 CCT6P1 2 ENSG00000228492RAB11FIP1P1 2 ENSG00000228784 LINC00954 2 ENSG00000229180 2ENSG00000229186 ADAM1A 2 ENSG00000230124 2 ENSG00000230373 GOLGA6L5P 2ENSG00000230454 2 ENSG00000230551 2 ENSG00000230606 2 ENSG00000230715 2ENSG00000232807 2 ENSG00000233137 2 ENSG00000233175 2 ENSG00000233184 2ENSG00000234072 2 ENSG00000234290 2 ENSG00000234353 2 ENSG00000234420ZNF37BP 2 ENSG00000234585 CCT6P3 2 ENSG00000234616 JRK 2 ENSG000002346312 ENSG00000234769 WASH4P 2 ENSG00000234771 2 ENSG00000234912 LINC00338 2ENSG00000235016 2 ENSG00000235194 PPP1R3E 2 ENSG00000235381 2ENSG00000235703 LINC00894 2 ENSG00000235999 2 ENSG00000236017 ASMTL-AS12 ENSG00000236088 COX10-AS1 2 ENSG00000236144 2 ENSG00000236255 2ENSG00000236287 ZBED5 2 ENSG00000236438 FAM157A 2 ENSG00000237298TTN-AS1 2 ENSG00000237441 RGL2 2 ENSG00000237491 2 ENSG00000238083LRRC37A2 2 ENSG00000239382 ALKBH6 2 ENSG00000239665 2 ENSG00000240038AMY2B 2 ENSG00000240053 LY6G5B 2 ENSG00000240288 GHRLOS 2ENSG00000240291 2 ENSG00000240731 2 ENSG00000241014 2 ENSG00000241058NSUN6 2 ENSG00000241404 EGFL8 2 ENSG00000241489 2 ENSG00000241528 2ENSG00000241769 LINC00893 2 ENSG00000242028 HYPK 2 ENSG00000242125 SNHG32 ENSG00000242282 2 ENSG00000242384 TBC1D3H 2 ENSG00000242802 AP5Z1 2ENSG00000242861 2 ENSG00000242866 STRC 2 ENSG00000243155 2ENSG00000243302 2 ENSG00000243452 NBPF15 2 ENSG00000243679 2ENSG00000243708 PLA2G4B 2 ENSG00000243716 NPIPB5 2 ENSG00000244119PDCL3P4 2 ENSG00000244151 2 ENSG00000244480 2 ENSG00000244560 2ENSG00000244754 N4BP2L2 2 ENSG00000244879 GABPB1-AS1 2 ENSG00000245149RNF139-AS1 2 ENSG00000245532 NEAT1 2 ENSG00000245849 RAD51-AS1 2ENSG00000245970 2 ENSG00000246090 2 ENSG00000246339 EXTL3-AS1 2ENSG00000246451 2 ENSG00000246922 UBAP1L 2 ENSG00000247679 2ENSG00000248019 FAM13A-AS1 2 ENSG00000248124 RRN3P1 2 ENSG00000249087C1orf213 2 ENSG00000250067 YJEFN3 2 ENSG00000250506 CDK3 2ENSG00000251022 THAP9-AS1 2 ENSG00000251136 2 ENSG00000251247 ZNF345 2ENSG00000251364 2 ENSG00000251369 ZNF550 2 ENSG00000251432 2ENSG00000251562 MALAT1 2 ENSG00000252690 SCARNA15 2 ENSG00000253106 2ENSG00000253200 2 ENSG00000253352 TUG1 2 ENSG00000254363 2ENSG00000254413 CHKB-CPT1B 2 ENSG00000254815 2 ENSG00000254995 STX16-NPEPL1 2 ENSG00000255031 2 ENSG00000255182 2 ENSG00000255717 SNHG1 2ENSG00000256028 2 ENSG00000256223 ZNF10 2 ENSG00000256294 ZNF225 2ENSG00000256525 POLG2 2 ENSG00000256667 KLRAP1 2 ENSG00000257511 2ENSG00000257621 2 ENSG00000258297 2 ENSG00000258311 2 ENSG00000258441LINC00641 2 ENSG00000258461 2 ENSG00000258472 2 ENSG00000258634 2ENSG00000258727 2 ENSG00000258839 MC1R 2 ENSG00000258890 CEP95 2ENSG00000259820 2 ENSG00000259865 2 ENSG00000259891 2 ENSG00000259972 2ENSG00000259994 2 ENSG00000260091 2 ENSG00000260236 2 ENSG00000260257 2ENSG00000260296 2 ENSG00000260306 2 ENSG00000260565 ERVK13-1 2ENSG00000260669 2 ENSG00000260711 2 ENSG00000260729 2 ENSG00000260772 2ENSG00000260778 MIR940 2 ENSG00000260837 2 ENSG00000260872 2ENSG00000260917 2 ENSG00000260924 2 ENSG00000260942 CAPN10-AS1 2ENSG00000261015 2 ENSG00000261052 SULT1A3 2 ENSG00000261067 2ENSG00000261087 2 ENSG00000261136 2 ENSG00000261139 2 ENSG00000261254 2ENSG00000261286 2 ENSG00000261324 2 ENSG00000261326 2 ENSG00000261355 2ENSG00000261408 TEN1-CDK3 2 ENSG00000261460 2 ENSG00000261488 2ENSG00000261490 2 ENSG00000261505 2 ENSG00000261526 2 ENSG00000261556 2ENSG00000261584 2 ENSG00000261613 2 ENSG00000261799 2 ENSG00000262580 2ENSG00000262877 2 ENSG00000263020 2 ENSG00000263126 2 ENSG00000263198 2ENSG00000263272 2 ENSG00000263276 2 ENSG00000263327 TAPT1-AS1 2ENSG00000264098 2 ENSG00000264112 2 ENSG00000264538 2 ENSG00000264772SNORA67 2 ENSG00000265298 2 ENSG00000265629 2 ENSG00000265690 2ENSG00000266086 2 ENSG00000266714 MYO15B 2 ENSG00000267152 2ENSG00000267244 2 ENSG00000267281 2 ENSG00000267283 2 ENSG00000267680ZNF224 2 ENSG00000267896 2 ENSG00000267940 2 ENSG00000268030 2ENSG00000268220 2 ENSG00000268471 MIR4453 2 ENSG00000269131 2ENSG00000269352 2 ENSG00000269399 2 ENSG00000269680 2 ENSG00000269751 2ENSG00000269821 KCNQ1OT1 2 ENSG00000269928 2 ENSG00000269929 2ENSG00000269958 2 ENSG00000270012 2 ENSG00000270015 2 ENSG00000270055 2ENSG00000270069 2 ENSG00000270189 2 ENSG00000270574 2 ENSG00000271344 2ENSG00000271430 2 ENSG00000271529 CICP14 2 ENSG00000271533 2ENSG00000271795 2 ENSG00000271816 2 ENSG00000271857 2 ENSG00000271870 2ENSG00000271895 2 ENSG00000271975 2 ENSG00000271997 2 ENSG00000272077 2ENSG00000272141 2 ENSG00000272145 NFYC-AS1 2 ENSG00000272216 2ENSG00000272316 2 ENSG00000272356 2 ENSG00000272455 2 ENSG00000272505 2ENSG00000272578 2 ENSG00000272589 ZSWIM8-AS1 2 ENSG00000272631 2ENSG00000272645 2 ENSG00000272658 2 ENSG00000272668 2 ENSG00000272720 2ENSG00000272752 STAG3L5P- PVRIG2P- PILRB 2 ENSG00000272782 2ENSG00000272849 2 ENSG00000272916 2 ENSG00000272977 2 ENSG00000273000 2ENSG00000273131 2 ENSG00000273137 2 ENSG00000273151 2 ENSG00000273271 2ENSG00000273373 2 ENSG00000273466 2 ENSG00000273478 3 ENSG00000067082KLF6 3 ENSG00000108551 RASD1 3 ENSG00000120129 DUSP1 3 ENSG00000120738EGR1 3 ENSG00000123358 NR4A1 3 ENSG00000125740 FOSB 3 ENSG00000128016ZFP36 3 ENSG00000128342 LIF 3 ENSG00000137331 IER3 3 ENSG00000139318DUSP6 3 ENSG00000142178 SIK1 3 ENSG00000148339 SLC25A25 3ENSG00000153234 NR4A2 3 ENSG00000158050 DUSP2 3 ENSG00000159388 BTG2 3ENSG00000160888 IER2 3 ENSG00000170345 FOS 3 ENSG00000171223 JUNB 3ENSG00000177606 JUN 3 ENSG00000198355 PIM3 4 ENSG00000062582 MRPS24 4ENSG00000065518 NDUFB4 4 ENSG00000090266 NDUFB2 4 ENSG00000099341 PSMD84 ENSG00000099795 NDUFB7 4 ENSG00000100216 TOMM22 4 ENSG00000103363TCEB2 4 ENSG00000106153 CHCHD2 4 ENSG00000110801 PSMD9 4 ENSG00000111639MRPL51 4 ENSG00000111775 COX6A1 4 ENSG00000112695 COX7A2 4ENSG00000116459 ATP5F1 4 ENSG00000119013 NDUFB3 4 ENSG00000120509 PDZD114 ENSG00000125356 NDUFA1 4 ENSG00000125445 MRPS7 4 ENSG00000125995 ROMO14 ENSG00000126267 COX6B1 4 ENSG00000126768 TIMM17B 4 ENSG00000127540UQCR11 4 ENSG00000127774 EMC6 4 ENSG00000131174 COX7B 4 ENSG00000135441BLOC1S1 4 ENSG00000135940 COX5B 4 ENSG00000136930 PSMB7 4ENSG00000140990 NDUFB10 4 ENSG00000141552 ANAPC11 4 ENSG00000141759TXNL4A 4 ENSG00000143977 SNRPG 4 ENSG00000145494 NDUFS6 4ENSG00000150779 TIMM8B 4 ENSG00000151366 NDUFC2 4 ENSG00000155368 DBI 4ENSG00000156411 C14orf2 4 ENSG00000163634 THOC7 4 ENSG00000164405 UQCRQ4 ENSG00000164919 COX6C 4 ENSG00000165264 NDUFB6 4 ENSG00000165283STOML2 4 ENSG00000166136 NDUFB8 4 ENSG00000169020 ATP5I 4ENSG00000169021 UQCRFS1 4 ENSG00000171421 MRPL36 4 ENSG00000172428MYEOV2 4 ENSG00000172586 CHCHD1 4 ENSG00000173436 MINOS1 4ENSG00000173915 USMG5 4 ENSG00000176340 COX8A 4 ENSG00000177700 POLR2L 4ENSG00000178307 TMEM11 4 ENSG00000178741 COX5A 4 ENSG00000183617 MRPL544 ENSG00000184076 UQCR10 4 ENSG00000184752 NDUFA12 4 ENSG00000185721DRG1 4 ENSG00000186010 NDUFA13 4 ENSG00000188612 SUMO2 4 ENSG00000189043NDUFA4 4 ENSG00000198522 GPN1 4 ENSG00000204922 C11orf83 4ENSG00000213619 NDUFS3 4 ENSG00000241468 ATP5J2 4 ENSG00000262814 MRPL125 ENSG00000000460 C1orf112 5 ENSG00000004142 POLDIP2 5 ENSG00000006634DBF4 5 ENSG00000007968 E2F2 5 ENSG00000010292 NCAPD2 5 ENSG00000011426ANLN 5 ENSG00000024526 DEPDC1 5 ENSG00000034063 UHRF1 5 ENSG00000040275SPDL1 5 ENSG00000048140 TSPAN17 5 ENSG00000049541 RFC2 5 ENSG00000051180RAD51 5 ENSG00000055044 NOP58 5 ENSG00000066279 ASPM 5 ENSG00000068489PRR11 5 ENSG00000072571 HMMR 5 ENSG00000075218 GTSE1 5 ENSG00000075702WDR62 5 ENSG00000077152 UBE2T 5 ENSG00000080986 NDC80 5 ENSG00000085840ORC1 5 ENSG00000085999 RAD54L 5 ENSG00000087111 PIGS 5 ENSG00000087586AURKA 5 ENSG00000088325 TPX2 5 ENSG00000089685 BIRC5 5 ENSG00000090889KIF4A 5 ENSG00000091651 ORC6 5 ENSG00000093009 CDC45 5 ENSG00000094804CDC6 5 ENSG00000097046 CDC7 5 ENSG00000100297 MCM5 5 ENSG00000100526CDKN3 5 ENSG00000100600 LGMN 5 ENSG00000101003 GINS1 5 ENSG00000101057MYBL2 5 ENSG00000101412 E2F1 5 ENSG00000101945 SUV39H1 5 ENSG00000102384CENPI 5 ENSG00000104064 GABPB1 5 ENSG00000104738 MCM4 5 ENSG00000104889RNASEH2A 5 ENSG00000105011 ASF1B 5 ENSG00000105135 ILVBL 5ENSG00000106462 EZH2 5 ENSG00000108106 UBE2S 5 ENSG00000109805 NCAPG 5ENSG00000111206 FOXM1 5 ENSG00000111247 RAD51AP1 5 ENSG00000111445 RFC55 ENSG00000111602 TIMELESS 5 ENSG00000112118 MCM3 5 ENSG00000112578 BYSL5 ENSG00000112742 TTK 5 ENSG00000112984 KIF20A 5 ENSG00000113368 LMNB1 5ENSG00000113810 SMC4 5 ENSG00000116212 LRRC42 5 ENSG00000116478 HDAC1 5ENSG00000116830 TTF2 5 ENSG00000117399 CDC20 5 ENSG00000117632 STMN1 5ENSG00000117724 CENPF 5 ENSG00000118193 KIF14 5 ENSG00000119969 HELLS 5ENSG00000120254 MTHFD1L 5 ENSG00000120539 MASTL 5 ENSG00000120647 CCDC775 ENSG00000120802 TMPO 5 ENSG00000121152 NCAPH 5 ENSG00000121621 KIF18A5 ENSG00000122483 CCDC18 5 ENSG00000122566 HNRNPA2B1 5 ENSG00000122952ZWINT 5 ENSG00000123219 CENPK 5 ENSG00000123416 TUBA1B 5 ENSG00000123485HJURP 5 ENSG00000123975 CKS2 5 ENSG00000124207 CSE1L 5 ENSG00000124766SOX4 5 ENSG00000125319 C17orf53 5 ENSG00000125944 HNRNPR 5ENSG00000126787 DLGAP5 5 ENSG00000127564 PKMYT1 5 ENSG00000128274 A4GALT5 ENSG00000128944 KNSTRN 5 ENSG00000129195 FAM64A 5 ENSG00000130202PVRL2 5 ENSG00000131153 GINS2 5 ENSG00000131269 ABCB7 5 ENSG00000131747TOP2A 5 ENSG00000132313 MRPL35 5 ENSG00000132646 PCNA 5 ENSG00000134057CCNB1 5 ENSG00000134690 CDCA8 5 ENSG00000135451 TROAP 5 ENSG00000135476ESPL1 5 ENSG00000135763 URB2 5 ENSG00000135823 STX6 5 ENSG00000136108CKAP2 5 ENSG00000136122 BORA 5 ENSG00000136492 BRIP1 5 ENSG00000136943CTSV 5 ENSG00000137449 CPEB2 5 ENSG00000137804 NUSAP1 5 ENSG00000137807KIF23 5 ENSG00000137812 CASC5 5 ENSG00000138092 CENPO 5 ENSG00000138160KIF11 5 ENSG00000138180 CEP55 5 ENSG00000138442 WDR12 5 ENSG00000138778CENPE 5 ENSG00000139618 BRCA2 5 ENSG00000139726 DENR 5 ENSG00000139734DIAPH3 5 ENSG00000140525 FANCI 5 ENSG00000142731 PLK4 5 ENSG00000142945KIF2C 5 ENSG00000143228 NUF2 5 ENSG00000143476 DTL 5 ENSG00000143493INTS7 5 ENSG00000143621 ILF2 5 ENSG00000143942 CHAC2 5 ENSG00000144554FANCD2 5 ENSG00000145386 CCNA2 5 ENSG00000145604 SKP2 5 ENSG00000145907G3BP1 5 ENSG00000146410 MTFR2 5 ENSG00000146670 CDCA5 5 ENSG00000146918NCAPG2 5 ENSG00000147140 NONO 5 ENSG00000147274 RBMX 5 ENSG00000147536GINS4 5 ENSG00000148773 MKI67 5 ENSG00000149554 CHEK1 5 ENSG00000151287TEX30 5 ENSG00000153044 CENPH 5 ENSG00000154839 SKA1 5 ENSG00000154920EME1 5 ENSG00000156970 BUB1B 5 ENSG00000157456 CCNB2 5 ENSG00000159259CHAF1B 5 ENSG00000161800 RACGAP1 5 ENSG00000161888 SPC24 5ENSG00000162062 C16orf59 5 ENSG00000162063 CCNF 5 ENSG00000163507KIAA1524 5 ENSG00000163808 KIF15 5 ENSG00000163923 RPL39L 5ENSG00000163950 SLBP 5 ENSG00000164045 CDC25A 5 ENSG00000164109 MAD2L1 5ENSG00000164611 PTTG1 5 ENSG00000165304 MELK 5 ENSG00000165480 SKA3 5ENSG00000166451 CENPN 5 ENSG00000166803 KIAA0101 5 ENSG00000166851 PLK15 ENSG00000167513 CDT1 5 ENSG00000167900 TK1 5 ENSG00000168078 PBK 5ENSG00000168393 DTYMK 5 ENSG00000168411 RFWD3 5 ENSG00000168496 FEN1 5ENSG00000168883 USP39 5 ENSG00000169607 CKAP2L 5 ENSG00000169679 BUB1 5ENSG00000170312 CDK1 5 ENSG00000171241 SHCBP1 5 ENSG00000171320 ESCO2 5ENSG00000171848 RRM2 5 ENSG00000173207 CKS1B 5 ENSG00000174442 ZWILCH 5ENSG00000175063 UBE2C 5 ENSG00000175216 CKAP5 5 ENSG00000175305 CCNE2 5ENSG00000176890 TYMS 5 ENSG00000177191 B3GNT8 5 ENSG00000178999 AURKB 5ENSG00000179051 RCC2 5 ENSG00000179115 FARSA 5 ENSG00000179632 MAF1 5ENSG00000182481 KPNA2 5 ENSG00000182628 SKA2 5 ENSG00000183763 TRAIP 5ENSG00000183814 LIN9 5 ENSG00000183856 IQGAP3 5 ENSG00000184661 CDCA2 5ENSG00000185480 PARPBP 5 ENSG00000186185 KIF18B 5 ENSG00000186871 ERCC6L5 ENSG00000187514 PTMA 5 ENSG00000187741 FANCA 5 ENSG00000188486 H2AFX 5ENSG00000188610 FAM72B 5 ENSG00000189057 FAM111B 5 ENSG00000196419 XRCC65 ENSG00000196550 FAM72A 5 ENSG00000196584 XRCC2 5 ENSG00000198331 HYLS15 ENSG00000198826 ARHGAP11A 5 ENSG00000198901 PRC1 5 ENSG00000203760CENPW 5 ENSG00000204392 LSM2 5 ENSG00000213186 TRIM59 5 ENSG00000215784FAM72D 5 ENSG00000228716 DHFR 5 ENSG00000237649 KIFC1 5 ENSG00000247077PGAM5 6 ENSG00000001460 STPG1 6 ENSG00000003096 KLHL13 6 ENSG00000003989SLC7A2 6 ENSG00000004838 ZMYND10 6 ENSG00000004848 ARX 6 ENSG00000005100DHX33 6 ENSG00000005448 WDR54 6 ENSG00000006740 ARHGAP44 6ENSG00000006837 CDKL3 6 ENSG00000007062 PROM1 6 ENSG00000007174 DNAH9 6ENSG00000007237 GAS7 6 ENSG00000007384 RHBDF1 6 ENSG00000007866 TEAD3 6ENSG00000008083 JARID2 6 ENSG00000010361 FUZ 6 ENSG00000010626 LRRC23 6ENSG00000011143 MKS1 6 ENSG00000011295 TTC19 6 ENSG00000011485 PPP5C 6ENSG00000016402 IL20RA 6 ENSG00000016864 GLT8D1 6 ENSG00000021300PLEKHB1 6 ENSG00000021645 NRXN3 6 ENSG00000024862 CCDC28A 6ENSG00000025156 HSF2 6 ENSG00000025772 TOMM34 6 ENSG00000026508 CD44 6ENSG00000032742 IFT88 6 ENSG00000034239 EFCAB1 6 ENSG00000036672 USP2 6ENSG00000037474 NSUN2 6 ENSG00000039139 DNAH5 6 ENSG00000042317 SPATA7 6ENSG00000043514 TRIT1 6 ENSG00000048342 CC2D2A 6 ENSG00000048471 SNX29 6ENSG00000048991 R3HDM1 6 ENSG00000049319 SRD5A2 6 ENSG00000049759 NEDD4L6 ENSG00000049769 PPP1R3F 6 ENSG00000050327 ARHGEF5 6 ENSG00000051341POLQ 6 ENSG00000054219 LY75 6 ENSG00000054282 SDCCAG8 6 ENSG00000054392HHAT 6 ENSG00000054983 GALC 6 ENSG00000056998 GYG2 6 ENSG00000057019DCBLD2 6 ENSG00000058085 LAMC2 6 ENSG00000064199 SPA17 6 ENSG00000064692SNCAIP 6 ENSG00000064999 ANKS1A 6 ENSG00000065357 DGKA 6 ENSG00000065491TBC1D22B 6 ENSG00000065970 FOXJ2 6 ENSG00000066084 DIP2B 6ENSG00000066185 ZMYND12 6 ENSG00000066248 NGEF 6 ENSG00000066629 EML1 6ENSG00000067208 EVI5 6 ENSG00000067369 TP53BP1 6 ENSG00000068650 ATP11A6 ENSG00000068885 IFT80 6 ENSG00000068971 PPP2R5B 6 ENSG00000070444 MNT6 ENSG00000070718 AP3M2 6 ENSG00000070731 ST6GALNAC2 6 ENSG00000070761C16orf80 6 ENSG00000071539 TRIP13 6 ENSG00000072133 RPS6KA6 6ENSG00000072422 RHOBTB1 6 ENSG00000073050 XRCC1 6 ENSG00000073464 CLCN46 ENSG00000074621 SLC24A1 6 ENSG00000074964 ARHGEF10L 6 ENSG00000075142SRI 6 ENSG00000075240 GRAMD4 6 ENSG00000075568 TMEM131 6 ENSG00000075945KIFAP3 6 ENSG00000077327 SPAG6 6 ENSG00000077514 POLD3 6 ENSG00000077800FKBP6 6 ENSG00000078246 TULP3 6 ENSG00000078487 ZCWPW1 6 ENSG00000078900TP73 6 ENSG00000079156 OSBPL6 6 ENSG00000079335 CDC14A 6 ENSG00000080298RFX3 6 ENSG00000080572 PIH1D3 6 ENSG00000080824 HSP90AA1 6ENSG00000081870 HSPB11 6 ENSG00000083290 ULK2 6 ENSG00000084764 MAPRE3 6ENSG00000085063 CD59 6 ENSG00000085433 WDR47 6 ENSG00000086102 NFX1 6ENSG00000086200 IPO11 6 ENSG00000087053 MTMR2 6 ENSG00000087152 ATXN7L36 ENSG00000087365 SF3B2 6 ENSG00000087510 TFAP2C 6 ENSG00000087903 RFX26 ENSG00000088053 GP6 6 ENSG00000088320 REM1 6 ENSG00000088727 KIF9 6ENSG00000088833 NSFL1C 6 ENSG00000088970 PLK1S1 6 ENSG00000088986 DYNLL16 ENSG00000089060 SLC8B1 6 ENSG00000089091 DZANK1 6 ENSG00000089101C20orf26 6 ENSG00000089123 TASP1 6 ENSG00000090273 NUDC 6ENSG00000090661 CERS4 6 ENSG00000090971 NAT14 6 ENSG00000091181 IL5RA 6ENSG00000092850 TEKT2 6 ENSG00000095261 PSMD5 6 ENSG00000095319 NUP188 6ENSG00000096433 ITPR3 6 ENSG00000096872 IFT74 6 ENSG00000100012 SEC14L36 ENSG00000100124 ANKRD54 6 ENSG00000100162 CENPM 6 ENSG00000100211 CBY16 ENSG00000100218 RTDR1 6 ENSG00000100228 RAB36 6 ENSG00000100271 TTLL16 ENSG00000100294 MCAT 6 ENSG00000100345 MYH9 6 ENSG00000100418 DESI1 6ENSG00000100422 CERK 6 ENSG00000100441 KHNYN 6 ENSG00000100462 PRMT5 6ENSG00000100490 CDKL1 6 ENSG00000100583 SAMD15 6 ENSG00000100591 AHSA1 6ENSG00000100625 SIX4 6 ENSG00000100784 RPS6KA5 6 ENSG00000101052 IFT52 6ENSG00000101222 SPEF1 6 ENSG00000101448 EPPIN 6 ENSG00000101928 MOSPD1 6ENSG00000102048 ASB9 6 ENSG00000102230 PCYT1B 6 ENSG00000102349 KLF8 6ENSG00000102466 FGF14 6 ENSG00000102543 CDADC1 6 ENSG00000102738 MRPS316 ENSG00000102743 SLC25A15 6 ENSG00000102781 KATNAL1 6 ENSG00000102886GDPD3 6 ENSG00000102996 MMP15 6 ENSG00000103021 CCDC113 6ENSG00000103042 SLC38A7 6 ENSG00000103160 HSDL1 6 ENSG00000103174 NAGPA6 ENSG00000103194 USP10 6 ENSG00000103260 METRN 6 ENSG00000103351 CLUAP16 ENSG00000103494 RPGRIP1L 6 ENSG00000103540 CCP110 6 ENSG00000103599IQCH 6 ENSG00000103647 CORO2B 6 ENSG00000103740 ACSBG1 6 ENSG00000103994ZNF106 6 ENSG00000103995 CEP152 6 ENSG00000104237 RP1 6 ENSG00000104361NIPAL2 6 ENSG00000104427 ZC2HC1A 6 ENSG00000104472 CHRAC1 6ENSG00000104490 NCALD 6 ENSG00000104549 SQLE 6 ENSG00000104723 TUSC3 6ENSG00000105258 POLR2I 6 ENSG00000105278 ZFR2 6 ENSG00000105519 CAPS 6ENSG00000105948 TTC26 6 ENSG00000105982 RNF32 6 ENSG00000106012 IQCE 6ENSG00000106049 HIBADH 6 ENSG00000106052 TAX1BP1 6 ENSG00000106125FAM188B 6 ENSG00000106399 RPA3 6 ENSG00000106459 NRF1 6 ENSG00000106477CEP41 6 ENSG00000106701 FSD1L 6 ENSG00000106992 AK1 6 ENSG00000107185RGP1 6 ENSG00000107186 MPDZ 6 ENSG00000107249 GLIS3 6 ENSG00000107521HPS1 6 ENSG00000107816 LZTS2 6 ENSG00000107957 SH3PXD2A 6ENSG00000108187 PBLD 6 ENSG00000108395 TRIM37 6 ENSG00000108406 DHX40 6ENSG00000108479 GALK1 6 ENSG00000108641 B9D1 6 ENSG00000108733 PEX12 6ENSG00000108753 HNF1B 6 ENSG00000108819 PPP1R9B 6 ENSG00000108946PRKAR1A 6 ENSG00000108947 EFNB3 6 ENSG00000109083 IFT20 6ENSG00000109171 SLAIN2 6 ENSG00000109501 WFS1 6 ENSG00000109680 TBC1D196 ENSG00000109685 WHSC1 6 ENSG00000109762 SNX25 6 ENSG00000109771 LRP2BP6 ENSG00000109944 C11orf63 6 ENSG00000110025 SNX15 6 ENSG00000110318KIAA1377 6 ENSG00000110841 PPFIBP1 6 ENSG00000111145 ELK3 6ENSG00000111218 PRMT8 6 ENSG00000111254 AKAP3 6 ENSG00000111262 KCNA1 6ENSG00000111321 LTBR 6 ENSG00000111325 OGFOD2 6 ENSG00000111450 STX2 6ENSG00000111554 MDM1 6 ENSG00000111647 UHRF1BP1L 6 ENSG00000111674 ENO26 ENSG00000111728 ST8SIA1 6 ENSG00000111834 RSPH4A 6 ENSG00000111837 MAK6 ENSG00000111877 MCM9 6 ENSG00000111879 FAM184A 6 ENSG00000111907TPD52L1 6 ENSG00000111961 SASH1 6 ENSG00000112183 RBM24 6ENSG00000112186 CAP2 6 ENSG00000112530 PACRG 6 ENSG00000112539 C6orf1186 ENSG00000112559 MDFI 6 ENSG00000112584 FAM120B 6 ENSG00000112667 DNPH16 ENSG00000112796 ENPP5 6 ENSG00000112981 NME5 6 ENSG00000113141 IK 6ENSG00000113318 MSH3 6 ENSG00000113456 RAD1 6 ENSG00000113583 C5orf15 6ENSG00000113645 WWC1 6 ENSG00000113946 CLDN16 6 ENSG00000113966 ARL6 6ENSG00000114446 IFT57 6 ENSG00000114455 HHLA2 6 ENSG00000114473 IQCG 6ENSG00000114656 KIAA1257 6 ENSG00000114670 NEK11 6 ENSG00000114805 PLCH16 ENSG00000114904 NEK4 6 ENSG00000115107 STEAP3 6 ENSG00000115145 STAM26 ENSG00000115216 NRBP1 6 ENSG00000115423 DNAH6 6 ENSG00000115425 PECR 6ENSG00000115486 GGCX 6 ENSG00000115685 PPP1R7 6 ENSG00000115750 TAF1B 6ENSG00000115947 ORC4 6 ENSG00000115970 THADA 6 ENSG00000115998 C2orf42 6ENSG00000116032 GRIN3B 6 ENSG00000116127 ALMS1 6 ENSG00000116128 BCL9 6ENSG00000116525 TRIM62 6 ENSG00000116675 DNAJC6 6 ENSG00000116793 PHTF16 ENSG00000116885 OSCP1 6 ENSG00000116957 TBCE 6 ENSG00000117016 RIMS3 6ENSG00000117477 CCDC181 6 ENSG00000117602 RCAN3 6 ENSG00000118096 IFT466 ENSG00000118307 CASC1 6 ENSG00000118407 FILIP1 6 ENSG00000118418 HMGN36 ENSG00000118420 UBE3D 6 ENSG00000118690 ARMC2 6 ENSG00000118965 WDR356 ENSG00000118997 DNAH7 6 ENSG00000119147 C2orf40 6 ENSG00000119328FAM206A 6 ENSG00000119333 WDR34 6 ENSG00000119397 CNTRL 6ENSG00000119401 TRIM32 6 ENSG00000119402 FBXW2 6 ENSG00000119636 CCDC1766 ENSG00000119640 ACYP1 6 ENSG00000119650 IFT43 6 ENSG00000119661 DNAL16 ENSG00000119685 TTLL5 6 ENSG00000119689 DLST 6 ENSG00000119698 PPP4R46 ENSG00000119703 ZC2HC1C 6 ENSG00000119782 FKBP1B 6 ENSG00000120051CCDC147 6 ENSG00000120055 C10orf95 6 ENSG00000120256 LRP11 6ENSG00000120262 CCDC170 6 ENSG00000120279 MYCT1 6 ENSG00000120306 CYSTM16 ENSG00000120658 ENOX1 6 ENSG00000120685 PROSER1 6 ENSG00000120694HSPH1 6 ENSG00000121057 AKAP1 6 ENSG00000121413 ZSCAN18 6ENSG00000121486 TRMT1L 6 ENSG00000121671 CRY2 6 ENSG00000122376 FAM35A 6ENSG00000122507 BBS9 6 ENSG00000122970 IFT81 6 ENSG00000123607 TTC21B 6ENSG00000123810 B9D2 6 ENSG00000123977 DAW1 6 ENSG00000124074 ENKD1 6ENSG00000124237 C20orf85 6 ENSG00000124678 TCP11 6 ENSG00000124749COL21A1 6 ENSG00000125124 BBS2 6 ENSG00000125384 PTGER2 6ENSG00000125409 TEKT3 6 ENSG00000125482 TTF1 6 ENSG00000125531 C20orf1956 ENSG00000125733 TRIP10 6 ENSG00000125779 PANK2 6 ENSG00000125871 MGME16 ENSG00000125968 ID1 6 ENSG00000125991 ERGIC3 6 ENSG00000126107 HECTD36 ENSG00000126391 FRMD8 6 ENSG00000126432 PRDX5 6 ENSG00000126773 PCNXL46 ENSG00000126777 KTN1 6 ENSG00000126778 SIX1 6 ENSG00000126870 WDR60 6ENSG00000127399 LRRC61 6 ENSG00000127824 TUBA4A 6 ENSG00000127863TNFRSF19 6 ENSG00000127914 AKAP9 6 ENSG00000127952 STYXL1 6ENSG00000128346 C22orf23 6 ENSG00000128408 RIBC2 6 ENSG00000128536 CDHR36 ENSG00000128581 RABL5 6 ENSG00000128607 KLHDC10 6 ENSG00000128881TTBK2 6 ENSG00000128891 C15orf57 6 ENSG00000129007 CALML4 6ENSG00000129028 THAP10 6 ENSG00000129151 BBOX1 6 ENSG00000129295 LRRC6 6ENSG00000129521 EGLN3 6 ENSG00000129654 FOXJ1 6 ENSG00000129951 6ENSG00000130177 CDC16 6 ENSG00000130363 RSPH3 6 ENSG00000130413 STK33 6ENSG00000130433 CACNG6 6 ENSG00000130511 SSBP4 6 ENSG00000130560 UBAC1 6ENSG00000130640 TUBGCP2 6 ENSG00000130762 ARHGEF16 6 ENSG00000130770ATPIF1 6 ENSG00000130962 PRRG1 6 ENSG00000131437 KIF3A 6 ENSG00000131470PSMC3IP 6 ENSG00000131697 NPHP4 6 ENSG00000131711 MAP1B 6ENSG00000131828 PDHA1 6 ENSG00000131848 ZSCAN5A 6 ENSG00000131941 RHPN26 ENSG00000131969 ABHD12B 6 ENSG00000132003 ZSWIM4 6 ENSG00000132004FBXW9 6 ENSG00000132010 ZNF20 6 ENSG00000132122 SPATA6 6 ENSG00000132139GAS2L2 6 ENSG00000132259 CNGA4 6 ENSG00000132321 IQCA1 6 ENSG00000132549VPS13B 6 ENSG00000132554 RGS22 6 ENSG00000132640 BTBD3 6 ENSG00000132664POLR3F 6 ENSG00000132768 DPH2 6 ENSG00000133056 PIK3C2B 6ENSG00000133065 SLC41A1 6 ENSG00000133104 SPG20 6 ENSG00000133115 STOML36 ENSG00000133131 MORC4 6 ENSG00000133216 EPHB2 6 ENSG00000133256 PDE6B6 ENSG00000133488 SEC14L4 6 ENSG00000133627 ACTR3B 6 ENSG00000133640LRRIQ1 6 ENSG00000133678 TMEM254 6 ENSG00000133739 LRRCC1 6ENSG00000133958 UNC79 6 ENSG00000134138 MEIS2 6 ENSG00000134247 PTGFRN 6ENSG00000135070 ISCA1 6 ENSG00000135205 CCDC146 6 ENSG00000135245 HILPDA6 ENSG00000135315 KIAA1009 6 ENSG00000135338 LCA5 6 ENSG00000135406 PRPH6 ENSG00000135519 KCNH3 6 ENSG00000135535 CD164 6 ENSG00000135537 LACE16 ENSG00000135549 PKIB 6 ENSG00000135597 REPS1 6 ENSG00000135931 ARMC9 6ENSG00000135951 TSGA10 6 ENSG00000135966 TGFBRAP1 6 ENSG00000136044APPL2 6 ENSG00000136319 TTC5 6 ENSG00000136448 NMT1 6 ENSG00000136449MYCBPAP 6 ENSG00000136451 VEZF1 6 ENSG00000136715 SAP130 6ENSG00000136811 ODF2 6 ENSG00000136918 WDR38 6 ENSG00000137266 SLC22A236 ENSG00000137274 BPHL 6 ENSG00000137414 FAM8A1 6 ENSG00000137434C6orf52 6 ENSG00000137473 TTC29 6 ENSG00000137494 ANKRD42 6ENSG00000137601 NEK1 6 ENSG00000137691 C11orf70 6 ENSG00000137707 BTG4 6ENSG00000137819 PAQR5 6 ENSG00000137821 LRRC49 6 ENSG00000137960 GIPC2 6ENSG00000138002 IFT172 6 ENSG00000138036 DYNC2LI1 6 ENSG00000138041SMEK2 6 ENSG00000138175 ARL3 6 ENSG00000138400 MDH1B 6 ENSG00000138433CIR1 6 ENSG00000138443 ABI2 6 ENSG00000138587 MNS1 6 ENSG00000138622HCN4 6 ENSG00000138640 FAM13A 6 ENSG00000138670 RASGEF1B 6ENSG00000138769 CDKL2 6 ENSG00000138771 SHROOM3 6 ENSG00000138823 MTTP 6ENSG00000139537 CCDC65 6 ENSG00000139624 CERS5 6 ENSG00000139714 MORN3 6ENSG00000139971 C14orf37 6 ENSG00000139974 SLC38A6 6 ENSG00000140025EFCAB11 6 ENSG00000140043 PTGR2 6 ENSG00000140057 AK7 6 ENSG00000140284SLC27A2 6 ENSG00000140403 DNAJA4 6 ENSG00000140463 BBS4 6ENSG00000140481 CCDC33 6 ENSG00000140527 WDR93 6 ENSG00000140564 FURIN 6ENSG00000140600 SH3GL3 6 ENSG00000140632 GLYR1 6 ENSG00000140876 NUDT7 6ENSG00000141012 GALNS 6 ENSG00000141013 GAS8 6 ENSG00000141098 GFOD2 6ENSG00000141294 LRRC46 6 ENSG00000141376 BCAS3 6 ENSG00000141499 WRAP536 ENSG00000141510 TP53 6 ENSG00000141580 WDR45B 6 ENSG00000141665 FBXO156 ENSG00000142621 FHAD1 6 ENSG00000142655 PEX14 6 ENSG00000142677IL22RA1 6 ENSG00000143093 STRIP1 6 ENSG00000143156 NME7 6ENSG00000143179 UCK2 6 ENSG00000143222 UFC1 6 ENSG00000143258 USP21 6ENSG00000143479 DYRK3 6 ENSG00000143499 SMYD2 6 ENSG00000143537 ADAM15 6ENSG00000143595 AQP10 6 ENSG00000143633 C1orf131 6 ENSG00000143653SCCPDH 6 ENSG00000143786 CNIH3 6 ENSG00000143933 CALM2 6 ENSG00000143951WDPCP 6 ENSG00000144061 NPHP1 6 ENSG00000144233 AMMECR1L 6ENSG00000144451 SPAG16 6 ENSG00000144504 ANKMY1 6 ENSG00000145075 CCDC396 ENSG00000145331 TRMT10A 6 ENSG00000145414 NAF1 6 ENSG00000145491ROPN1L 6 ENSG00000145945 FAM50B 6 ENSG00000145982 FARS2 6ENSG00000146038 DCDC2 6 ENSG00000146083 RNF44 6 ENSG00000146221 TCTE1 6ENSG00000146233 CYP39A1 6 ENSG00000146242 TPBG 6 ENSG00000146243IRAK1BP1 6 ENSG00000146376 ARHGAP18 6 ENSG00000146722 6 ENSG00000146729GBAS 6 ENSG00000146733 PSPH 6 ENSG00000146856 AGBL3 6 ENSG00000147003TMEM27 6 ENSG00000147117 ZNF157 6 ENSG00000147202 DIAPH2 6ENSG00000147224 PRPS1 6 ENSG00000147231 CXorf57 6 ENSG00000147316 MCPH16 ENSG00000147400 CETN2 6 ENSG00000147457 CHMP7 6 ENSG00000147894C9orf72 6 ENSG00000148057 IDNK 6 ENSG00000148219 ASTN2 6 ENSG00000148225WDR31 6 ENSG00000148660 CAMK2G 6 ENSG00000148814 LRRC27 6ENSG00000148842 CNNM2 6 ENSG00000149050 ZNF214 6 ENSG00000149179C11orf49 6 ENSG00000149201 CCDC81 6 ENSG00000149292 TTC12 6ENSG00000149300 C11orf52 6 ENSG00000149328 GLB1L2 6 ENSG00000149480 MTA26 ENSG00000149573 MPZL2 6 ENSG00000149782 PLCB3 6 ENSG00000150281 CTF1 6ENSG00000150433 TMEM218 6 ENSG00000150456 N6AMT2 6 ENSG00000150628SPATA4 6 ENSG00000150667 FSIP1 6 ENSG00000150764 DIXDC1 6ENSG00000150773 PIH1D2 6 ENSG00000150873 C2orf50 6 ENSG00000151023 ENKUR6 ENSG00000151065 DCP1B 6 ENSG00000151320 AKAP6 6 ENSG00000151338 MIPOL16 ENSG00000151413 NUBPL 6 ENSG00000151445 VIPAS39 6 ENSG00000151575 TEX96 ENSG00000151689 INPP1 6 ENSG00000151773 CCDC122 6 ENSG00000151779 NBAS6 ENSG00000152076 CCDC74B 6 ENSG00000152464 RPP38 6 ENSG00000152503TRIM36 6 ENSG00000152582 SPEF2 6 ENSG00000152611 CAPSL 6 ENSG00000152763WDR78 6 ENSG00000152936 IFLTD1 6 ENSG00000153132 CLGN 6 ENSG00000153140CETN3 6 ENSG00000153237 CCDC148 6 ENSG00000153347 FAM81B 6ENSG00000153531 ADPRHL1 6 ENSG00000153558 FBXL2 6 ENSG00000153560 UBP1 6ENSG00000153714 LURAP1L 6 ENSG00000153774 CFDP1 6 ENSG00000153789 FAM92B6 ENSG00000153832 FBXO36 6 ENSG00000153896 ZNF599 6 ENSG00000153904DDAH1 6 ENSG00000153930 ANKFN1 6 ENSG00000154124 FAM105B 6ENSG00000154153 FAM134B 6 ENSG00000154240 CEP112 6 ENSG00000154380 ENAH6 ENSG00000154479 CCDC173 6 ENSG00000154556 SORBS2 6 ENSG00000154760SLFN13 6 ENSG00000154917 RAB6B 6 ENSG00000154930 ACSS1 6 ENSG00000155026RSPH10B 6 ENSG00000155085 AK9 6 ENSG00000155096 AZIN1 6 ENSG00000155189AGPAT5 6 ENSG00000155530 LRGUK 6 ENSG00000155666 KDM8 6 ENSG00000155749ALS2CR12 6 ENSG00000155761 SPAG17 6 ENSG00000155816 FMN2 6ENSG00000155974 GRIP1 6 ENSG00000156030 ELMSAN1 6 ENSG00000156049 GNA146 ENSG00000156050 FAM161B 6 ENSG00000156171 DRAM2 6 ENSG00000156172C8orf37 6 ENSG00000156206 C15orf26 6 ENSG00000156232 WHAMM 6ENSG00000156299 TIAM1 6 ENSG00000156313 RPGR 6 ENSG00000156463 SH3RF2 6ENSG00000156958 GALK2 6 ENSG00000157227 MMP14 6 ENSG00000157330 C1orf1586 ENSG00000157423 HYDIN 6 ENSG00000157429 ZNF19 6 ENSG00000157470 FAM81A6 ENSG00000157538 DSCR3 6 ENSG00000157578 LCA5L 6 ENSG00000157653C9orf43 6 ENSG00000157796 WDR19 6 ENSG00000157856 DRC1 6 ENSG00000157869RAB28 6 ENSG00000158023 WDR66 6 ENSG00000158113 LRRC43 6 ENSG00000158122AAED1 6 ENSG00000158234 FAIM 6 ENSG00000158296 SLC13A3 6 ENSG00000158423RIBC1 6 ENSG00000158428 C2orf62 6 ENSG00000158445 KCNB1 6ENSG00000158486 DNAH3 6 ENSG00000158669 AGPAT6 6 ENSG00000158850 B4GALT36 ENSG00000159079 C21orf59 6 ENSG00000159239 C2orf81 6 ENSG00000159685CHCHD6 6 ENSG00000159713 TPPP3 6 ENSG00000159714 ZDHHC1 6ENSG00000160051 IQCC 6 ENSG00000160145 KALRN 6 ENSG00000160183 TMPRSS3 6ENSG00000160188 RSPH1 6 ENSG00000160345 C9orf116 6 ENSG00000160613 PCSK76 ENSG00000160753 RUSC1 6 ENSG00000160803 UBQLN4 6 ENSG00000160949 TONSL6 ENSG00000160991 ORAI2 6 ENSG00000161036 LRWD1 6 ENSG00000161040 FBXL136 ENSG00000161326 DUSP14 6 ENSG00000161328 LRRC56 6 ENSG00000161513 FDXR6 ENSG00000161905 ALOX15 6 ENSG00000162040 HS3ST6 6 ENSG00000162105SHANK2 6 ENSG00000162148 PPP1R32 6 ENSG00000162302 RPS6KA4 6ENSG00000162543 UBXN10 6 ENSG00000162598 C1orf87 6 ENSG00000162600 OMA16 ENSG00000162616 DNAJB4 6 ENSG00000162620 LRRIQ3 6 ENSG00000162643WDR63 6 ENSG00000162755 KLHDC9 6 ENSG00000162769 FLVCR1 6ENSG00000162814 SPATA17 6 ENSG00000162999 DUSP19 6 ENSG00000163001CCDC104 6 ENSG00000163006 CCDC138 6 ENSG00000163040 CCDC74A 6ENSG00000163060 TEKT4 6 ENSG00000163071 SPATA18 6 ENSG00000163075 6ENSG00000163083 INHBB 6 ENSG00000163093 BBS5 6 ENSG00000163125 RPRD2 6ENSG00000163138 PACRGL 6 ENSG00000163214 DHX57 6 ENSG00000163251 FZD5 6ENSG00000163263 C1orf189 6 ENSG00000163322 FAM175A 6 ENSG00000163349HIPK1 6 ENSG00000163491 NEK10 6 ENSG00000163512 AZI2 6 ENSG00000163521GLB1L 6 ENSG00000163576 EFHB 6 ENSG00000163596 ICA1L 6 ENSG00000163617KIAA1407 6 ENSG00000163624 CDS1 6 ENSG00000163655 GMPS 6 ENSG00000163686ABHD6 6 ENSG00000163818 LZTFL1 6 ENSG00000163875 MEAF6 6 ENSG00000163879DNALI1 6 ENSG00000164002 EXO5 6 ENSG00000164099 PRSS12 6 ENSG00000164114MAP9 6 ENSG00000164118 CEP44 6 ENSG00000164185 ZNF474 6 ENSG00000164306PRIMPOL 6 ENSG00000164402 8-Sep 6 ENSG00000164404 GDF9 6 ENSG00000164411GJB7 6 ENSG00000164440 TXLNB 6 ENSG00000164465 DCBLD1 6 ENSG00000164542KIAA0895 6 ENSG00000164627 KIF6 6 ENSG00000164674 SYTL3 6ENSG00000164675 IQUB 6 ENSG00000164746 C7orf57 6 ENSG00000164758 MED30 6ENSG00000164818 HEATR2 6 ENSG00000164938 TP53INP1 6 ENSG00000164953TMEM67 6 ENSG00000164970 FAM219A 6 ENSG00000164972 C9orf24 6ENSG00000165029 ABCA1 6 ENSG00000165084 C8orf34 6 ENSG00000165097 KDM1B6 ENSG00000165118 C9orf64 6 ENSG00000165124 SVEP1 6 ENSG00000165164CXorf22 6 ENSG00000165185 KIAA1958 6 ENSG00000165209 STRBP 6ENSG00000165219 GAPVD1 6 ENSG00000165309 ARMC3 6 ENSG00000165383 LRRC186 ENSG00000165506 DNAAF2 6 ENSG00000165533 TTC8 6 ENSG00000165695 AK8 6ENSG00000165698 C9orf9 6 ENSG00000165724 ZMYND19 6 ENSG00000165730 STOX16 ENSG00000165807 PPP1R36 6 ENSG00000166165 CKB 6 ENSG00000166171 DPCD 6ENSG00000166173 LARP6 6 ENSG00000166246 C16orf71 6 ENSG00000166262FAM227B 6 ENSG00000166263 STXBP4 6 ENSG00000166275 C10orf32 6ENSG00000166311 SMPD1 6 ENSG00000166313 APBB1 6 ENSG00000166323 C11orf656 ENSG00000166352 C11orf74 6 ENSG00000166402 TUB 6 ENSG00000166435 XRRA16 ENSG00000166455 C16orf46 6 ENSG00000166526 ZNF3 6 ENSG00000166578 IQCD6 ENSG00000166592 RRAD 6 ENSG00000166596 WDR16 6 ENSG00000166946 CCNDBP16 ENSG00000166959 MS4A8 6 ENSG00000166963 MAP1A 6 ENSG00000167065 DUSP186 ENSG00000167094 TTC16 6 ENSG00000167113 COQ4 6 ENSG00000167131 CCDC1036 ENSG00000167136 ENDOG 6 ENSG00000167186 COQ7 6 ENSG00000167216 KATNAL26 ENSG00000167523 SPATA33 6 ENSG00000167550 RHEBL1 6 ENSG00000167552TUBA1A 6 ENSG00000167646 DNAAF3 6 ENSG00000167733 HSD11B1L 6ENSG00000167740 CYB5D2 6 ENSG00000167858 TEKT1 6 ENSG00000167904 TMEM686 ENSG00000167962 ZNF598 6 ENSG00000168014 C2CD3 6 ENSG00000168038 ULK46 ENSG00000168314 MOBP 6 ENSG00000168350 DEGS2 6 ENSG00000168487 BMP1 6ENSG00000168575 SLC20A2 6 ENSG00000168589 DYNLRB2 6 ENSG00000168658VWA3B 6 ENSG00000168675 LDLRAD4 6 ENSG00000168734 PKIG 6 ENSG00000168754FAM178B 6 ENSG00000168772 CXXC4 6 ENSG00000168778 TCTN2 6ENSG00000168884 TNIP2 6 ENSG00000168938 PPIC 6 ENSG00000169064 ZBBX 6ENSG00000169126 ARMC4 6 ENSG00000169189 NSMCE1 6 ENSG00000169213 RAB3B 6ENSG00000169379 ARL13B 6 ENSG00000169550 MUC15 6 ENSG00000169902 TPST1 6ENSG00000169905 TOR1AIP2 6 ENSG00000170231 FABP6 6 ENSG00000170264FAM161A 6 ENSG00000170270 C14orf142 6 ENSG00000170469 SPATA24 6ENSG00000170482 SLC23A1 6 ENSG00000170509 HSD17B13 6 ENSG00000170871KIAA0232 6 ENSG00000170959 DCDC1 6 ENSG00000171132 PRKCE 6ENSG00000171160 MORN4 6 ENSG00000171174 RBKS 6 ENSG00000171428 NAT1 6ENSG00000171517 LPAR3 6 ENSG00000171533 MAP6 6 ENSG00000171574 ZNF584 6ENSG00000171595 DNAI2 6 ENSG00000171757 LRRC34 6 ENSG00000171793 CTPS1 6ENSG00000171798 KNDC1 6 ENSG00000171885 AQP4 6 ENSG00000171962 LRRC48 6ENSG00000172164 SNTB1 6 ENSG00000172301 COPRS 6 ENSG00000172361 CCDC11 6ENSG00000172426 RSPH9 6 ENSG00000172578 KLHL6 6 ENSG00000172671 ZFAND4 6ENSG00000172955 ADH6 6 ENSG00000173013 CCDC96 6 ENSG00000173208 ABCD2 6ENSG00000173226 IQCB1 6 ENSG00000173627 APOBEC4 6 ENSG00000173838 10-Mar6 ENSG00000173947 PIFO 6 ENSG00000174007 CEP19 6 ENSG00000174132 FAM174A6 ENSG00000174156 GSTA3 6 ENSG00000174343 CHRNA9 6 ENSG00000174456C12orf76 6 ENSG00000174483 BBS1 6 ENSG00000174586 ZNF497 6ENSG00000174628 IQCK 6 ENSG00000174705 SH3PXD2B 6 ENSG00000174776 WDR496 ENSG00000174796 THAP6 6 ENSG00000174808 BTC 6 ENSG00000174898 CATSPERD6 ENSG00000175279 APITD1 6 ENSG00000175376 EIF1AD 6 ENSG00000175664TEX26 6 ENSG00000175697 GPR156 6 ENSG00000175792 RUVBL1 6ENSG00000175970 UNC119B 6 ENSG00000176040 TMPRSS7 6 ENSG00000176171BNIP3 6 ENSG00000176209 SMIM19 6 ENSG00000176381 PRR18 6 ENSG00000176401EID2B 6 ENSG00000176485 PLA2G16 6 ENSG00000176563 CNTD1 6ENSG00000176601 MAP3K19 6 ENSG00000176714 CCDC121 6 ENSG00000176986SEC24C 6 ENSG00000177103 DSCAML1 6 ENSG00000177112 MRVI1-AS1 6ENSG00000177398 UMODL1 6 ENSG00000177459 C8orf47 6 ENSG00000177508 IRX36 ENSG00000177640 CASC2 6 ENSG00000177674 AGTRAP 6 ENSG00000177994C2orf73 6 ENSG00000178053 MLF1 6 ENSG00000178075 GRAMD1C 6ENSG00000178125 PPP1R42 6 ENSG00000178149 DALRD3 6 ENSG00000178425NT5DC1 6 ENSG00000178460 MCMDC2 6 ENSG00000178467 P4HTM 6ENSG00000178568 ERBB4 6 ENSG00000178665 ZNF713 6 ENSG00000178732 GP5 6ENSG00000178796 RIIAD1 6 ENSG00000178965 C1orf173 6 ENSG00000179029TMEM107 6 ENSG00000179071 CCDC89 6 ENSG00000179133 C10orf67 6ENSG00000179195 ZNF664 6 ENSG00000179240 6 ENSG00000179598 PLD6 6ENSG00000179813 FAM216B 6 ENSG00000179902 C1orf194 6 ENSG00000180098TRNAU1AP 6 ENSG00000180263 FGD6 6 ENSG00000180346 TIGD2 6ENSG00000180481 GLIPR1L2 6 ENSG00000180509 KCNE1 6 ENSG00000180769WDFY3-AS2 6 ENSG00000180787 ZFP3 6 ENSG00000180914 OXTR 6ENSG00000181004 BBS12 6 ENSG00000181322 NME9 6 ENSG00000181481 RNF135 6ENSG00000181619 GPR135 6 ENSG00000182093 WRB 6 ENSG00000182224 CYB5D1 6ENSG00000182329 6 ENSG00000182504 CEP97 6 ENSG00000182518 FAM104B 6ENSG00000182768 NGRN 6 ENSG00000182957 SPATA13 6 ENSG00000183117 CSMD1 6ENSG00000183161 FANCF 6 ENSG00000183207 RUVBL2 6 ENSG00000183273 CCDC606 ENSG00000183323 CCDC125 6 ENSG00000183346 C10orf107 6 ENSG00000183578TNFAIP8L3 6 ENSG00000183628 DGCR6 6 ENSG00000183644 C11orf88 6ENSG00000183690 EFHC2 6 ENSG00000183784 C9orf66 6 ENSG00000183826 BTBD96 ENSG00000183831 ANKRD45 6 ENSG00000183914 DNAH2 6 ENSG00000183941HIST2H4A 6 ENSG00000184154 LRTOMT 6 ENSG00000184349 EFNA5 6ENSG00000184385 C21orf128 6 ENSG00000184500 PROS1 6 ENSG00000184613NELL2 6 ENSG00000184702 5-Sep 6 ENSG00000184731 FAM110C 6ENSG00000184886 PIGW 6 ENSG00000184898 RBM43 6 ENSG00000184939 ZFP90 6ENSG00000184986 TMEM121 6 ENSG00000185055 EFCAB10 6 ENSG00000185158LRRC37B 6 ENSG00000185220 PGBD2 6 ENSG00000185222 WBP5 6 ENSG00000185250PPIL6 6 ENSG00000185261 KIAA0825 6 ENSG00000185267 CDNF 6ENSG00000185305 ARL15 6 ENSG00000185361 TNFAIP8L1 6 ENSG00000185379RAD51D 6 ENSG00000185420 SMYD3 6 ENSG00000185608 MRPL40 6ENSG00000185681 MORN5 6 ENSG00000185875 THNSL1 6 ENSG00000185989 RASA3 6ENSG00000186094 AGBL4 6 ENSG00000186104 CYP2R1 6 ENSG00000186132 C2orf766 ENSG00000186198 SLC51B 6 ENSG00000186231 KLHL32 6 ENSG00000186314PRELID2 6 ENSG00000186329 TMEM212 6 ENSG00000186352 ANKRD37 6ENSG00000186471 AKAP14 6 ENSG00000186496 ZNF396 6 ENSG00000186523FAM86B1 6 ENSG00000186625 KATNA1 6 ENSG00000186638 KIF24 6ENSG00000186687 LYRM7 6 ENSG00000186889 TMEM17 6 ENSG00000186952 TMEM2326 ENSG00000186973 FAM183A 6 ENSG00000186976 EFCAB6 6 ENSG00000187079TEAD1 6 ENSG00000187122 SLIT1 6 ENSG00000187189 TSPYL4 6 ENSG00000187240DYNC2H1 6 ENSG00000187260 WDR86 6 ENSG00000187535 IFT140 6ENSG00000187624 C17orf97 6 ENSG00000187642 C1orf170 6 ENSG00000187695 6ENSG00000187726 DNAJB13 6 ENSG00000187733 AMY1C 6 ENSG00000188010 MORN26 ENSG00000188039 NWD1 6 ENSG00000188229 TUBB4B 6 ENSG00000188316 ENO4 6ENSG00000188352 FOCAD 6 ENSG00000188396 TCTEX1D4 6 ENSG00000188452 CERKL6 ENSG00000188523 C9orf171 6 ENSG00000188596 C12orf55 6 ENSG00000188659FAM154B 6 ENSG00000188817 SNTN 6 ENSG00000188921 PTPLAD2 6ENSG00000188931 C1orf192 6 ENSG00000189157 FAM47E 6 ENSG00000196090PTPRT 6 ENSG00000196169 KIF19 6 ENSG00000196230 TUBB 6 ENSG00000196236XPNPEP3 6 ENSG00000196277 GRM7 6 ENSG00000196437 ZNF569 6ENSG00000196476 C20orf96 6 ENSG00000196482 ESRRG 6 ENSG00000196535MYO18A 6 ENSG00000196659 TTC30B 6 ENSG00000196693 ZNF33B 6ENSG00000196704 AMZ2 6 ENSG00000196814 MVB12B 6 ENSG00000196872KIAA1211L 6 ENSG00000196890 HIST3H2BB 6 ENSG00000197057 DTHD1 6ENSG00000197122 SRC 6 ENSG00000197168 NEK5 6 ENSG00000197208 SLC22A4 6ENSG00000197580 BCO2 6 ENSG00000197584 KCNMB2 6 ENSG00000197603 C5orf426 ENSG00000197653 DNAH10 6 ENSG00000197748 WDR96 6 ENSG00000197826C4orf22 6 ENSG00000197889 MEIG1 6 ENSG00000197980 LEKR1 6ENSG00000198003 CCDC151 6 ENSG00000198088 NUP62CL 6 ENSG00000198125 MB 6ENSG00000198157 HMGN5 6 ENSG00000198182 ZNF607 6 ENSG00000198551 ZNF6276 ENSG00000198553 KCNRG 6 ENSG00000198624 CCDC69 6 ENSG00000198668 CALM16 ENSG00000198718 FAM179B 6 ENSG00000198729 PPP1R14C 6 ENSG00000198815FOXJ3 6 ENSG00000198825 INPP5F 6 ENSG00000198860 TSEN15 6ENSG00000198894 CIPC 6 ENSG00000198919 DZIP3 6 ENSG00000198945 L3MBTL3 6ENSG00000198947 DMD 6 ENSG00000198960 ARMCX6 6 ENSG00000203301 6ENSG00000203372 6 ENSG00000203485 INF2 6 ENSG00000203499 FAM83H-AS1 6ENSG00000203666 EFCAB2 6 ENSG00000203705 TATDN3 6 ENSG00000203734 ECT2L6 ENSG00000203778 FAM229B 6 ENSG00000203797 DDO 6 ENSG00000203865ATP1A1OS 6 ENSG00000203965 EFCAB7 6 ENSG00000203985 LDLRAD1 6ENSG00000204052 LRRC73 6 ENSG00000204070 SYS1 6 ENSG00000204104 TRAF3IP16 ENSG00000204356 NELFE 6 ENSG00000204390 HSPA1L 6 ENSG00000204428LY6G5C 6 ENSG00000204438 GPANK1 6 ENSG00000204566 C10orf115 6ENSG00000204599 TRIM39 6 ENSG00000204666 6 ENSG00000204682 CASC10 6ENSG00000204711 C9orf135 6 ENSG00000204815 TTC25 6 ENSG00000204852 TCTN16 ENSG00000204860 FAM201A 6 ENSG00000204950 LRRC10B 6 ENSG00000205084TMEM231 6 ENSG00000205129 C4orf47 6 ENSG00000205231 TTLL10-AS1 6ENSG00000205240 OR7E36P 6 ENSG00000205593 DENND6B 6 ENSG00000205730ITPRIPL2 6 ENSG00000205758 CRYZL1 6 ENSG00000205808 PPAPDC2 6ENSG00000205930 C21orf49 6 ENSG00000206053 HN1L 6 ENSG00000206199 ANKUB16 ENSG00000206567 6 ENSG00000213085 CCDC19 6 ENSG00000213123 TCTEX1D2 6ENSG00000213297 ZNF625- ZNF20 6 ENSG00000213533 TMEM110 6ENSG00000213753 CENPBD1P1 6 ENSG00000213904 LIPE-AS1 6 ENSG00000213937CLDN9 6 ENSG00000214114 MYCBP 6 ENSG00000214174 AMZ2P1 6 ENSG00000214413BBIP1 6 ENSG00000214447 FAM187A 6 ENSG00000214575 CPEB1 6ENSG00000214706 IFRD2 6 ENSG00000215187 FAM166B 6 ENSG00000215217C5orf49 6 ENSG00000215475 SIAH3 6 ENSG00000215845 TSTD1 6ENSG00000219626 FAM228B 6 ENSG00000221821 C6orf226 6 ENSG00000221838AP4M1 6 ENSG00000221995 TIAF1 6 ENSG00000222046 DCDC2B 6 ENSG000002233436 ENSG00000223547 ZNF844 6 ENSG00000223658 6 ENSG00000224038 6ENSG00000224049 6 ENSG00000224165 DNAJC27- AS1 6 ENSG00000224281SLC25A5-AS1 6 ENSG00000224479 6 ENSG00000224699 LAMTOR5- AS1 6ENSG00000225302 6 ENSG00000225361 PPP1R26-AS1 6 ENSG00000225377 6ENSG00000225431 6 ENSG00000225766 6 ENSG00000226026 6 ENSG00000226137BAIAP2-AS1 6 ENSG00000226471 6 ENSG00000226644 6 ENSG00000226711 FAM66C6 ENSG00000226754 6 ENSG00000227084 6 ENSG00000227308 6 ENSG00000227630LINC01132 6 ENSG00000227695 DNMBP-AS1 6 ENSG00000227877 LINC00948 6ENSG00000228084 6 ENSG00000228242 6 ENSG00000228723 SRGAP3-AS2 6ENSG00000228858 6 ENSG00000228889 UBAC2-AS1 6 ENSG00000229124 VIM-AS1 6ENSG00000229980 TOB1-AS1 6 ENSG00000230062 ANKRD66 6 ENSG00000230873STMND1 6 ENSG00000230943 6 ENSG00000231023 LINC00326 6 ENSG00000231028LINC00271 6 ENSG00000231043 6 ENSG00000231621 6 ENSG00000231738 TSPAN196 ENSG00000231980 6 ENSG00000232415 6 ENSG00000232453 6 ENSG00000232859LYRM9 6 ENSG00000232862 6 ENSG00000233170 6 ENSG00000233382 NKAPP1 6ENSG00000233730 6 ENSG00000233936 6 ENSG00000234465 PINLYP 6ENSG00000234478 6 ENSG00000234684 SDCBP2-AS1 6 ENSG00000234911 TEX21P 6ENSG00000235106 LINC00094 6 ENSG00000235142 6 ENSG00000235162 C12orf75 6ENSG00000235453 TOPORS-AS1 6 ENSG00000235527 6 ENSG00000236914 6ENSG00000237188 6 ENSG00000239467 6 ENSG00000240137 6 ENSG00000240204SMKR1 6 ENSG00000240875 LINC00886 6 ENSG00000241935 HOGA1 6ENSG00000241990 6 ENSG00000242808 SOX2-OT 6 ENSG00000242852 ZNF709 6ENSG00000243069 ARHGEF26- AS1 6 ENSG00000243627 6 ENSG00000243660 ZNF4876 ENSG00000243667 WDR92 6 ENSG00000243701 LINC00883 6 ENSG00000243710WDR65 6 ENSG00000243836 WDR86-AS1 6 ENSG00000243910 TUBA4B 6ENSG00000244968 LIFR-AS1 6 ENSG00000245025 6 ENSG00000245248 USP2-AS1 6ENSG00000245317 6 ENSG00000245573 BDNF-AS 6 ENSG00000245694 CRNDE 6ENSG00000245750 6 ENSG00000246016 6 ENSG00000246250 6 ENSG00000246308 6ENSG00000246705 H2AFJ 6 ENSG00000247081 6 ENSG00000247271 ZBED5-AS1 6ENSG00000247311 6 ENSG00000247363 6 ENSG00000247746 USP51 6ENSG00000247796 6 ENSG00000247853 6 ENSG00000248008 DYNLL1-AS1 6ENSG00000248508 SRP14-AS1 6 ENSG00000248712 CCDC153 6 ENSG00000248801 6ENSG00000248905 FMN1 6 ENSG00000248932 6 ENSG00000249042 6ENSG00000249241 6 ENSG00000249348 UGDH-AS1 6 ENSG00000249481 SPATS1 6ENSG00000249610 6 ENSG00000249621 6 ENSG00000250056 LINC01018 6ENSG00000250462 LRRC37BP1 6 ENSG00000250510 GPR162 6 ENSG00000250790 6ENSG00000251307 6 ENSG00000251503 APITD1-CORT 6 ENSG00000251602 6ENSG00000251669 FAM86EP 6 ENSG00000253302 STAU2-AS1 6 ENSG00000253320 6ENSG00000253379 6 ENSG00000253719 ATXN7L3B 6 ENSG00000253948 6ENSG00000254024 6 ENSG00000254389 RHPN1-AS1 6 ENSG00000254473 6ENSG00000254608 6 ENSG00000254837 6 ENSG00000255036 6 ENSG00000255277ABCC6P2 6 ENSG00000256061 DYX1C1 6 ENSG00000256073 C21orf119 6ENSG00000257057 LINC01171 6 ENSG00000257084 6 ENSG00000257108 NHLRC4 6ENSG00000257542 OR7E47P 6 ENSG00000257698 6 ENSG00000258334 6ENSG00000258539 6 ENSG00000258701 LINC00638 6 ENSG00000258940 6ENSG00000259087 6 ENSG00000259225 6 ENSG00000259251 6 ENSG00000259264 6ENSG00000259319 6 ENSG00000259426 6 ENSG00000259577 6 ENSG00000259802 6ENSG00000259901 6 ENSG00000260018 6 ENSG00000260057 6 ENSG00000260136 6ENSG00000260328 6 ENSG00000260372 AQP4-AS1 6 ENSG00000260517 6ENSG00000260526 6 ENSG00000260604 6 ENSG00000260643 6 ENSG00000260908 6ENSG00000260951 6 ENSG00000261188 6 ENSG00000261572 6 ENSG00000261652C15orf65 6 ENSG00000261759 6 ENSG00000261777 6 ENSG00000263011 6ENSG00000263812 LINC00908 6 ENSG00000265666 6 ENSG00000265688 MAFG-AS1 6ENSG00000265752 6 ENSG00000266947 6 ENSG00000267100 ILF3-AS1 6ENSG00000267106 C19orf82 6 ENSG00000267128 RNF157-AS1 6 ENSG000002673486 ENSG00000267390 6 ENSG00000267439 6 ENSG00000267848 6 ENSG00000268061NAPA-AS1 6 ENSG00000268175 6 ENSG00000268565 6 ENSG00000269916 6ENSG00000270021 6 ENSG00000270362 HMGN3-AS1 6 ENSG00000270504 6ENSG00000270820 6 ENSG00000271133 6 ENSG00000271853 6 ENSG00000272079 6ENSG00000272086 6 ENSG00000272106 6 ENSG00000272143 FGF14-AS2 6ENSG00000272168 CASC15 6 ENSG00000272288 6 ENSG00000272323 6ENSG00000272442 6 ENSG00000272502 6 ENSG00000272514 6 ENSG00000272831 6ENSG00000272902 6 ENSG00000273061 6 ENSG00000273071 7 ENSG00000008988RPS20 7 ENSG00000063046 EIF4B 7 ENSG00000063177 RPL18 7 ENSG00000071082RPL31 7 ENSG00000083845 RPS5 7 ENSG00000084090 STARD7 7 ENSG00000089009RPL6 7 ENSG00000089157 RPLP0 7 ENSG00000089289 IGBP1 7 ENSG00000100129EIF3L 7 ENSG00000100316 RPL3 7 ENSG00000100353 EIF3D 7 ENSG00000100814CCNB1IP1 7 ENSG00000104408 EIF3E 7 ENSG00000104529 EEF1D 7ENSG00000105193 RPS16 7 ENSG00000105202 FBL 7 ENSG00000105372 RPS19 7ENSG00000105373 GLTSCR2 7 ENSG00000105640 RPL18A 7 ENSG00000107625 DDX507 ENSG00000108107 RPL28 7 ENSG00000108298 RPL19 7 ENSG00000108604SMARCD2 7 ENSG00000109475 RPL34 7 ENSG00000110700 RPS13 7ENSG00000111678 C12orf57 7 ENSG00000112306 RPS12 7 ENSG00000114391 RPL247 ENSG00000114942 EEF1B2 7 ENSG00000115268 RPS15 7 ENSG00000116251 RPL227 ENSG00000117543 DPH5 7 ENSG00000118181 RPS25 7 ENSG00000118816 CCNI 7ENSG00000122026 RPL21 7 ENSG00000122406 RPL5 7 ENSG00000124614 RPS10 7ENSG00000125691 RPL23 7 ENSG00000125743 SNRPD2 7 ENSG00000126088 UROD 7ENSG00000129158 SERGEF 7 ENSG00000130159 ECSIT 7 ENSG00000130255 RPL36 7ENSG00000130312 MRPL34 7 ENSG00000131143 COX4I1 7 ENSG00000131469 RPL277 ENSG00000133112 TPT1 7 ENSG00000134419 RPS15A 7 ENSG00000135390 ATP5G27 ENSG00000136104 RNASEH2B 7 ENSG00000136710 CCDC115 7 ENSG00000136942RPL35 7 ENSG00000137054 POLR1E 7 ENSG00000137154 RPS6 7 ENSG00000137818RPLP1 7 ENSG00000137970 RPL7P9 7 ENSG00000138326 RPS24 7 ENSG00000139239RPL14P1 7 ENSG00000140905 GCSH 7 ENSG00000140988 RPS2 7 ENSG00000142534RPS11 7 ENSG00000142541 RPL13A 7 ENSG00000142676 RPL11 7 ENSG00000142937RPS8 7 ENSG00000143947 RPS27A 7 ENSG00000144713 RPL32 7 ENSG00000144741SLC25A26 7 ENSG00000145425 RPS3A 7 ENSG00000145592 RPL37 7ENSG00000145741 BTF3 7 ENSG00000147403 RPL10 7 ENSG00000147604 RPL7 7ENSG00000147654 EBAG9 7 ENSG00000147677 EIF3H 7 ENSG00000148303 RPL7A 7ENSG00000149273 RPS3 7 ENSG00000149806 FAU 7 ENSG00000151353 TMEM18 7ENSG00000156482 RPL30 7 ENSG00000156508 EEF1A1 7 ENSG00000156853 ZNF6897 ENSG00000161016 RPL8 7 ENSG00000161970 RPL26 7 ENSG00000162244 RPL29 7ENSG00000163344 PMVK 7 ENSG00000163682 RPL9 7 ENSG00000164587 RPS14 7ENSG00000166441 RPL27A 7 ENSG00000166902 MRPL16 7 ENSG00000167526 RPL137 ENSG00000168028 RPSA 7 ENSG00000169100 SLC25A6 7 ENSG00000169714 CNBP7 ENSG00000170889 RPS9 7 ENSG00000171858 RPS21 7 ENSG00000171863 RPS7 7ENSG00000172809 RPL38 7 ENSG00000173726 TOMM20 7 ENSG00000174444 RPL4 7ENSG00000174547 MRPL11 7 ENSG00000174748 RPL15 7 ENSG00000175061FAM211A- AS1 7 ENSG00000175390 EIF3F 7 ENSG00000177410 ZFAS1 7ENSG00000177600 RPLP2 7 ENSG00000177954 RPS27 7 ENSG00000178464 7ENSG00000182774 RPS17L 7 ENSG00000182899 RPL35A 7 ENSG00000183405 RPS7P17 ENSG00000184779 RPS17 7 ENSG00000185641 7 ENSG00000186468 RPS23 7ENSG00000188243 COMMD6 7 ENSG00000188846 RPL14 7 ENSG00000189343 RPS2P467 ENSG00000196205 EEF1A1P5 7 ENSG00000196531 NACA 7 ENSG00000196683TOMM7 7 ENSG00000197756 RPL37A 7 ENSG00000197958 RPL12 7 ENSG00000198034RPS4X 7 ENSG00000198242 RPL23A 7 ENSG00000198546 ZNF511 7ENSG00000198755 RPL10A 7 ENSG00000198918 RPL39 7 ENSG00000204196 7ENSG00000204387 C6orf48 7 ENSG00000204628 GNB2L1 7 ENSG00000205246RPSAP58 7 ENSG00000212802 RPL15P3 7 ENSG00000213178 7 ENSG00000213442RPL18AP3 7 ENSG00000213553 RPLP0P6 7 ENSG00000213741 RPS29 7ENSG00000213860 RPL21P75 7 ENSG00000214046 SMIM7 7 ENSG00000214113 LYRM47 ENSG00000214389 RPS3AP26 7 ENSG00000214485 RPL7P1 7 ENSG00000214784 7ENSG00000215021 PHB2 7 ENSG00000218426 7 ENSG00000220749 RPL21P28 7ENSG00000220842 7 ENSG00000221983 UBA52 7 ENSG00000226084 7ENSG00000226221 7 ENSG00000227063 RPL41P1 7 ENSG00000227081 7ENSG00000229117 RPL41 7 ENSG00000229638 RPL4P4 7 ENSG00000230629 RPS23P87 ENSG00000231500 RPS18 7 ENSG00000232472 EEF1B2P3 7 ENSG00000232573RPL3P4 7 ENSG00000233476 EEF1A1P6 7 ENSG00000233762 7 ENSG00000233913 7ENSG00000233927 RPS28 7 ENSG00000234741 GAS5 7 ENSG00000234797 RPS3AP6 7ENSG00000234851 7 ENSG00000235065 RPL24P2 7 ENSG00000235552 RPL6P27 7ENSG00000236552 RPL13AP5 7 ENSG00000240087 7 ENSG00000240342 RPS2P5 7ENSG00000241343 RPL36A 7 ENSG00000242071 RPL7AP6 7 ENSG00000242299 7ENSG00000243199 7 ENSG00000244313 7 ENSG00000244398 7 ENSG00000244716 7ENSG00000245910 SNHG6 7 ENSG00000254772 EEF1G 7 ENSG00000265681 RPL17 7ENSG00000269893 SNHG8 8 ENSG00000000938 FGR 8 ENSG00000005844 ITGAL 8ENSG00000006074 CCL18 8 ENSG00000006075 CCL3 8 ENSG00000008516 MMP25 8ENSG00000009790 TRAF3IP3 8 ENSG00000010295 IFFO1 8 ENSG00000010671 BTK 8ENSG00000010810 FYN 8 ENSG00000011600 TYROBP 8 ENSG00000012779 ALOX5 8ENSG00000013725 CD6 8 ENSG00000015285 WAS 8 ENSG00000018280 SLC11A1 8ENSG00000019169 MARCO 8 ENSG00000023902 PLEKHO1 8 ENSG00000026297RNASET2 8 ENSG00000027869 SH2D2A 8 ENSG00000028137 TNFRSF1B 8ENSG00000033327 GAB2 8 ENSG00000038945 MSR1 8 ENSG00000043462 LCP2 8ENSG00000048740 CELF2 8 ENSG00000054967 RELT 8 ENSG00000057657 PRDM1 8ENSG00000059377 TBXAS1 8 ENSG00000059728 MXD1 8 ENSG00000059804 SLC2A3 8ENSG00000062282 DGAT2 8 ENSG00000064201 TSPAN32 8 ENSG00000065413ANKRD44 8 ENSG00000065675 PRKCQ 8 ENSG00000066294 CD84 8 ENSG00000066336SPI1 8 ENSG00000068831 RASGRP2 8 ENSG00000069424 KCNAB2 8ENSG00000072401 UBE2D1 8 ENSG00000072694 FCGR2B 8 ENSG00000072786 STK108 ENSG00000072818 ACAP1 8 ENSG00000073921 PICALM 8 ENSG00000074706IPCEF1 8 ENSG00000074966 TXK 8 ENSG00000075624 ACTB 8 ENSG00000075884ARHGAP15 8 ENSG00000076641 PAG1 8 ENSG00000076662 ICAM3 8ENSG00000076928 ARHGEF1 8 ENSG00000077420 APBB1IP 8 ENSG00000077984 CST78 ENSG00000078589 P2RY10 8 ENSG00000079263 SP140 8 ENSG00000081059 TCF78 ENSG00000081087 OSTM1 8 ENSG00000081237 PTPRC 8 ENSG00000081320 STK17B8 ENSG00000082074 FYB 8 ENSG00000085265 FCN1 8 ENSG00000085514 PILRA 8ENSG00000086300 SNX10 8 ENSG00000086730 LAT2 8 ENSG00000087266 SH3BP2 8ENSG00000088827 SIGLEC1 8 ENSG00000089327 FXYD5 8 ENSG00000089639 GMIP 8ENSG00000089820 ARHGAP4 8 ENSG00000090339 ICAM1 8 ENSG00000090674 MCOLN18 ENSG00000091106 NLRC4 8 ENSG00000092929 UNC13D 8 ENSG00000095303 PTGS18 ENSG00000095370 SH2D3C 8 ENSG00000096996 IL12RB1 8 ENSG00000099308MAST3 8 ENSG00000099985 OSM 8 ENSG00000100055 CYTH4 8 ENSG00000100060MFNG 8 ENSG00000100351 GRAP2 8 ENSG00000100365 NCF4 8 ENSG00000100368CSF2RB 8 ENSG00000100385 IL2RB 8 ENSG00000100599 RIN3 8 ENSG00000100985MMP9 8 ENSG00000101109 STK4 8 ENSG00000101265 RASSF2 8 ENSG00000101307SIRPB1 8 ENSG00000101336 HCK 8 ENSG00000101916 TLR8 8 ENSG00000102032RENBP 8 ENSG00000102218 RP2 8 ENSG00000102445 KIAA0226L 8ENSG00000102524 TNFSF13B 8 ENSG00000102575 ACP5 8 ENSG00000102879 CORO1A8 ENSG00000103005 USB1 8 ENSG00000103187 COTL1 8 ENSG00000103313 MEFV 8ENSG00000103522 IL21R 8 ENSG00000103569 AQP9 8 ENSG00000104814 MAP4K1 8ENSG00000104894 CD37 8 ENSG00000104972 LILRB1 8 ENSG00000104998 IL27RA 8ENSG00000105122 RASAL3 8 ENSG00000105329 TGFB1 8 ENSG00000105339 DENND38 ENSG00000105483 CARD8 8 ENSG00000105639 JAK3 8 ENSG00000105835 NAMPT 8ENSG00000105851 PIK3CG 8 ENSG00000105967 TFEC 8 ENSG00000106066 CPVL 8ENSG00000106348 IMPDH1 8 ENSG00000107099 DOCK8 8 ENSG00000107485 GATA3 8ENSG00000107551 RASSF4 8 ENSG00000108405 P2RX1 8 ENSG00000108932 SLC16A68 ENSG00000108960 MMD 8 ENSG00000109743 BST1 8 ENSG00000110031 LPXN 8ENSG00000110047 EHD1 8 ENSG00000110077 MS4A6A 8 ENSG00000110079 MS4A4A 8ENSG00000110324 IL10RA 8 ENSG00000110395 CBL 8 ENSG00000110446 SLC15A3 8ENSG00000110448 CD5 8 ENSG00000110848 CD69 8 ENSG00000110876 SELPLG 8ENSG00000110934 BIN2 8 ENSG00000111252 SH2B3 8 ENSG00000111348 ARHGDIB 8ENSG00000111679 PTPN6 8 ENSG00000111729 CLEC4A 8 ENSG00000112096 SOD2 8ENSG00000112137 PHACTR1 8 ENSG00000112149 CD83 8 ENSG00000112195 TREML28 ENSG00000112303 VNN2 8 ENSG00000112531 QKI 8 ENSG00000112799 LY86 8ENSG00000113263 ITK 8 ENSG00000113273 ARSB 8 ENSG00000114013 CD86 8ENSG00000114450 GNB4 8 ENSG00000114626 ABTB1 8 ENSG00000114737 CISH 8ENSG00000115085 ZAP70 8 ENSG00000115165 CYTIP 8 ENSG00000115232 ITGA4 8ENSG00000115271 GCA 8 ENSG00000115318 LOXL3 8 ENSG00000115325 DOK1 8ENSG00000115355 CCDC88A 8 ENSG00000115604 IL18R1 8 ENSG00000115607IL18RAP 8 ENSG00000115756 HPCAL1 8 ENSG00000115828 QPCT 8ENSG00000115935 WIPF1 8 ENSG00000115956 PLEK 8 ENSG00000116017 ARID3A 8ENSG00000116337 AMPD2 8 ENSG00000116701 NCF2 8 ENSG00000116741 RGS2 8ENSG00000116824 CD2 8 ENSG00000116852 KIF21B 8 ENSG00000117009 KMO 8ENSG00000117090 SLAMF1 8 ENSG00000117091 CD48 8 ENSG00000117115 PADI2 8ENSG00000117281 CD160 8 ENSG00000118263 KLF7 8 ENSG00000118508 RAB32 8ENSG00000119321 FKBP15 8 ENSG00000119535 CSF3R 8 ENSG00000119686 FLVCR28 ENSG00000120063 GNA13 8 ENSG00000120709 FAM53C 8 ENSG00000120899 PTK2B8 ENSG00000121060 TRIM25 8 ENSG00000121210 KIAA0922 8 ENSG00000121281ADCY7 8 ENSG00000121797 CCRL2 8 ENSG00000121807 CCR2 8 ENSG00000121966CXCR4 8 ENSG00000122122 SASH3 8 ENSG00000122188 LAX1 8 ENSG00000122224LY9 8 ENSG00000122862 SRGN 8 ENSG00000122986 HVCN1 8 ENSG00000123329ARHGAP9 8 ENSG00000123338 NCKAP1L 8 ENSG00000123689 G0S2 8ENSG00000124126 PREX1 8 ENSG00000124203 ZNF831 8 ENSG00000124334 IL9R 8ENSG00000124357 NAGK 8 ENSG00000124491 F13A1 8 ENSG00000124731 TREM1 8ENSG00000125354 6-Sep 8 ENSG00000125538 IL1B 8 ENSG00000125637 PSD4 8ENSG00000125735 TNFSF14 8 ENSG00000125910 S1PR4 8 ENSG00000126246 IGFLR18 ENSG00000126262 FFAR2 8 ENSG00000126264 HCST 8 ENSG00000126353 CCR7 8ENSG00000126561 STAT5A 8 ENSG00000126860 EVI2A 8 ENSG00000126882 FAM78A8 ENSG00000127084 FGD3 8 ENSG00000127152 BCL11B 8 ENSG00000127507 EMR2 8ENSG00000127951 FGL2 8 ENSG00000128271 ADORA2A 8 ENSG00000128340 RAC2 8ENSG00000128383 APOBEC3A 8 ENSG00000128815 WDFY4 8 ENSG00000129071 MBD48 ENSG00000129226 CD68 8 ENSG00000129277 CCL4 8 ENSG00000129657 SEC14L18 ENSG00000129675 ARHGEF6 8 ENSG00000130203 APOE 8 ENSG00000130208 APOC18 ENSG00000130429 ARPC1B 8 ENSG00000130475 FCHO1 8 ENSG00000130592 LSP18 ENSG00000130755 GMFG 8 ENSG00000130775 THEMIS2 8 ENSG00000130830 MPP18 ENSG00000131042 LILRB2 8 ENSG00000131378 RFTN1 8 ENSG00000131401 NAPSB8 ENSG00000131669 NINJ1 8 ENSG00000131724 IL13RA1 8 ENSG00000132182NUP210 8 ENSG00000132205 EMILIN2 8 ENSG00000132334 PTPRE 8ENSG00000132510 KDM6B 8 ENSG00000132514 CLEC10A 8 ENSG00000132965ALOX5AP 8 ENSG00000133048 CHI3L1 8 ENSG00000133246 PRAM1 8ENSG00000133574 GIMAP4 8 ENSG00000133961 NUMB 8 ENSG00000134242 PTPN22 8ENSG00000134516 DOCK2 8 ENSG00000134668 SPOCD1 8 ENSG00000134686 PHC2 8ENSG00000134698 AGO4 8 ENSG00000134830 C5AR2 8 ENSG00000134954 ETS1 8ENSG00000135074 ADAM19 8 ENSG00000135077 HAVCR2 8 ENSG00000135218 CD36 8ENSG00000135426 TESPA1 8 ENSG00000135439 AGAP2 8 ENSG00000135604 STX11 8ENSG00000135636 DYSF 8 ENSG00000135838 NPL 8 ENSG00000135905 DOCK10 8ENSG00000136040 PLXNC1 8 ENSG00000136111 TBC1D4 8 ENSG00000136167 LCP1 8ENSG00000136250 AOAH 8 ENSG00000136286 MYO1G 8 ENSG00000136404 TM6SF1 8ENSG00000136490 LIMD2 8 ENSG00000136560 TANK 8 ENSG00000136867 SLC31A2 8ENSG00000136869 TLR4 8 ENSG00000137076 TLN1 8 ENSG00000137078 SIT1 8ENSG00000137265 IRF4 8 ENSG00000137462 TLR2 8 ENSG00000137491 SLCO2B1 8ENSG00000137575 SDCBP 8 ENSG00000137752 CASP1 8 ENSG00000137841 PLCB2 8ENSG00000138378 STAT4 8 ENSG00000138621 PPCDC 8 ENSG00000138964 PARVG 8ENSG00000139193 CD27 8 ENSG00000139278 GLIPR1 8 ENSG00000139370 SLC15A48 ENSG00000139436 GIT2 8 ENSG00000140030 GPR65 8 ENSG00000140368 PSTPIP18 ENSG00000140379 BCL2A1 8 ENSG00000140678 ITGAX 8 ENSG00000140749 IGSF68 ENSG00000140931 CMTM3 8 ENSG00000140968 IRF8 8 ENSG00000141293 SKAP1 8ENSG00000141298 SSH2 8 ENSG00000141480 ARRB2 8 ENSG00000141506 PIK3R5 8ENSG00000141576 RNF157 8 ENSG00000142185 TRPM2 8 ENSG00000142227 EMP3 8ENSG00000142347 MYO1F 8 ENSG00000142512 SIGLEC10 8 ENSG00000143110C1orf162 8 ENSG00000143119 CD53 8 ENSG00000143226 FCGR2A 8ENSG00000143382 ADAMTSL4 8 ENSG00000143546 S100A8 8 ENSG00000143851PTPN7 8 ENSG00000144218 AFF3 8 ENSG00000144815 NXPE3 8 ENSG000001454161-Mar 8 ENSG00000145569 FAM105A 8 ENSG00000145649 GZMA 8 ENSG00000145819ARHGAP26 8 ENSG00000146070 PLA2G7 8 ENSG00000146094 DOK3 8ENSG00000146112 PPP1R18 8 ENSG00000146192 FGD2 8 ENSG00000146278 PNRC1 8ENSG00000146285 SCML4 8 ENSG00000146592 CREB5 8 ENSG00000146859 TMEM1408 ENSG00000147010 SH3KBP1 8 ENSG00000147065 MSN 8 ENSG00000147168 IL2RG8 ENSG00000147251 DOCK11 8 ENSG00000147416 ATP6V1B2 8 ENSG00000147443DOK2 8 ENSG00000147454 SLC25A37 8 ENSG00000147459 DOCK5 8ENSG00000147872 PLIN2 8 ENSG00000148572 NRBF2 8 ENSG00000148908 RGS10 8ENSG00000149091 DGKZ 8 ENSG00000149177 PTPRJ 8 ENSG00000149781 FERMT3 8ENSG00000150337 FCGR1A 8 ENSG00000150681 RGS18 8 ENSG00000150867 PIP4K2A8 ENSG00000151490 PTPRO 8 ENSG00000151651 ADAM8 8 ENSG00000151702 FLI1 8ENSG00000151726 ACSL1 8 ENSG00000151948 GLT1D1 8 ENSG00000152213 ARL11 8ENSG00000152270 PDE3B 8 ENSG00000152495 CAMK4 8 ENSG00000153071 DAB2 8ENSG00000153179 RASSF3 8 ENSG00000153283 CD96 8 ENSG00000153317 ASAP1 8ENSG00000153395 LPCAT1 8 ENSG00000153563 CD8A 8 ENSG00000154016 GRAP 8ENSG00000154451 GBP5 8 ENSG00000154589 LY96 8 ENSG00000155307 SAMSN1 8ENSG00000155465 SLC7A7 8 ENSG00000155629 PIK3AP1 8 ENSG00000155659 VSIG48 ENSG00000155849 ELMO1 8 ENSG00000155926 SLA 8 ENSG00000156273 BACH1 8ENSG00000157350 ST3GAL2 8 ENSG00000157551 KCNJ15 8 ENSG00000158517 NCF18 ENSG00000158714 SLAMF8 8 ENSG00000158869 FCER1G 8 ENSG00000159189 C1QC8 ENSG00000159322 ADPGK 8 ENSG00000159618 GPR114 8 ENSG00000159753 RLTPR8 ENSG00000160185 UBASH3A 8 ENSG00000160219 GAB3 8 ENSG00000160255 ITGB28 ENSG00000160326 SLC2A6 8 ENSG00000160593 AMICA1 8 ENSG00000160654 CD3G8 ENSG00000160883 HK3 8 ENSG00000160999 SH2B2 8 ENSG00000161570 CCL5 8ENSG00000161791 FMNL3 8 ENSG00000161929 SCIMP 8 ENSG00000162511 LAPTM5 8ENSG00000162676 GFI1 8 ENSG00000162711 NLRP3 8 ENSG00000162739 SLAMF6 8ENSG00000163154 TNFAIP8L2 8 ENSG00000163162 RNF149 8 ENSG00000163219ARHGAP25 8 ENSG00000163220 S100A9 8 ENSG00000163376 KBTBD8 8ENSG00000163421 PROK2 8 ENSG00000163464 CXCR1 8 ENSG00000163519 TRAT1 8ENSG00000163563 MNDA 8 ENSG00000163564 PYHIN1 8 ENSG00000163600 ICOS 8ENSG00000163823 CCR1 8 ENSG00000164691 TAGAP 8 ENSG00000165030 NFIL3 8ENSG00000165168 CYBB 8 ENSG00000165178 NCF1C 8 ENSG00000166128 RAB8B 8ENSG00000166340 TPP1 8 ENSG00000166501 PRKCB 8 ENSG00000166523 CLEC4E 8ENSG00000166716 ZNF592 8 ENSG00000166927 MS4A7 8 ENSG00000167208 SNX20 8ENSG00000167261 DPEP2 8 ENSG00000167286 CD3D 8 ENSG00000167483 FAM129C 8ENSG00000167613 LAIR1 8 ENSG00000167680 SEMA6B 8 ENSG00000167851 CD300A8 ENSG00000168067 MAP4K2 8 ENSG00000168071 CCDC88B 8 ENSG00000168404MLKL 8 ENSG00000168421 RHOH 8 ENSG00000168685 IL7R 8 ENSG00000168918INPP5D 8 ENSG00000169180 XPO6 8 ENSG00000169220 RGS14 8 ENSG00000169228RAB24 8 ENSG00000169403 PTAFR 8 ENSG00000169413 RNASE6 8 ENSG00000169442CD52 8 ENSG00000169508 GPR183 8 ENSG00000169554 ZEB2 8 ENSG00000169826CSGALNACT2 8 ENSG00000169896 ITGAM 8 ENSG00000170323 FABP4 8ENSG00000170458 CD14 8 ENSG00000170525 PFKFB3 8 ENSG00000170542 SERPINB98 ENSG00000170909 OSCAR 8 ENSG00000170956 CEACAM3 8 ENSG00000171049 FPR28 ENSG00000171051 FPR1 8 ENSG00000171488 LRRC8C 8 ENSG00000171608 PIK3CD8 ENSG00000171659 GPR34 8 ENSG00000171700 RGS19 8 ENSG00000171777RASGRP4 8 ENSG00000171860 C3AR1 8 ENSG00000172081 MOB3A 8ENSG00000172116 CD8B 8 ENSG00000172216 CEBPB 8 ENSG00000172243 CLEC7A 8ENSG00000172322 CLEC12A 8 ENSG00000172349 IL16 8 ENSG00000172543 CTSW 8ENSG00000172575 RASGRP1 8 ENSG00000172673 THEMIS 8 ENSG00000173020ADRBK1 8 ENSG00000173110 HSPA6 8 ENSG00000173200 PARP15 8ENSG00000173281 PPP1R3B 8 ENSG00000173369 C1QB 8 ENSG00000173372 C1QA 8ENSG00000173391 OLR1 8 ENSG00000173535 TNFRSF10C 8 ENSG00000173559 NABP18 ENSG00000173638 SLC19A1 8 ENSG00000173757 STAT5B 8 ENSG00000173762 CD78 ENSG00000173868 PHOSPHO1 8 ENSG00000174004 NRROS 8 ENSG00000174125TLR1 8 ENSG00000174579 MSL2 8 ENSG00000174600 CMKLR1 8 ENSG00000174718KIAA1551 8 ENSG00000175463 TBC1D10C 8 ENSG00000175489 LRRC25 8ENSG00000175857 GAPT 8 ENSG00000176390 CRLF3 8 ENSG00000177105 RHOG 8ENSG00000177575 CD163 8 ENSG00000177663 IL17RA 8 ENSG00000177885 GRB2 8ENSG00000178562 CD28 8 ENSG00000178607 ERN1 8 ENSG00000179361 ARID3B 8ENSG00000180096 1-Sep 8 ENSG00000180353 HCLS1 8 ENSG00000180448 HMHA1 8ENSG00000180871 CXCR2 8 ENSG00000180953 ST20 8 ENSG00000181381 DDX60L 8ENSG00000181409 AATK 8 ENSG00000181631 P2RY13 8 ENSG00000182022 CHST15 8ENSG00000182287 AP1S2 8 ENSG00000182487 NCF1B 8 ENSG00000182511 FES 8ENSG00000182578 CSF1R 8 ENSG00000182866 LCK 8 ENSG00000182885 GPR97 8ENSG00000183019 C19orf59 8 ENSG00000183023 SLC8A1 8 ENSG00000183484GPR132 8 ENSG00000183688 FAM101B 8 ENSG00000183748 8 ENSG00000183918SH2D1A 8 ENSG00000184014 DENND5A 8 ENSG00000184060 ADAP2 8ENSG00000184371 CSF1 8 ENSG00000184588 PDE4B 8 ENSG00000184602 SNN 8ENSG00000184730 APOBR 8 ENSG00000184922 FMNL1 8 ENSG00000185201 IFITM2 8ENSG00000185215 TNFAIP2 8 ENSG00000185339 TCN2 8 ENSG00000185477 GPRIN38 ENSG00000185811 IKZF1 8 ENSG00000185862 EVI2B 8 ENSG00000185947 ZNF2678 ENSG00000186074 CD300LF 8 ENSG00000186469 GNG2 8 ENSG00000186517ARHGAP30 8 ENSG00000186635 ARAP1 8 ENSG00000186818 LILRB4 8ENSG00000187116 LILRA5 8 ENSG00000187239 FNBP1 8 ENSG00000187474 FPR3 8ENSG00000187688 TRPV2 8 ENSG00000187764 SEMA4D 8 ENSG00000187796 CARD9 8ENSG00000187994 RINL 8 ENSG00000188404 SELL 8 ENSG00000188820 FAM26F 8ENSG00000188895 MSL1 8 ENSG00000188906 LRRK2 8 ENSG00000189067 LITAF 8ENSG00000196511 TPK1 8 ENSG00000196549 MME 8 ENSG00000196663 TECPR2 8ENSG00000196843 ARID5A 8 ENSG00000196954 CASP4 8 ENSG00000197081 IGF2R 8ENSG00000197249 SERPINA1 8 ENSG00000197471 SPN 8 ENSG00000197629 MPEG1 8ENSG00000197860 SGTB 8 ENSG00000197872 FAM49A 8 ENSG00000198053 SIRPA 8ENSG00000198223 CSF2RA 8 ENSG00000198286 CARD11 8 ENSG00000198771 RCSD18 ENSG00000198821 CD247 8 ENSG00000198837 DENND4B 8 ENSG00000198846 TOX8 ENSG00000198851 CD3E 8 ENSG00000198879 SFMBT2 8 ENSG00000203747 FCGR3A8 ENSG00000204136 GGTA1P 8 ENSG00000204160 ZDHHC18 8 ENSG00000204267TAP2 8 ENSG00000204397 CARD16 8 ENSG00000204472 AIF1 8 ENSG00000204482LST1 8 ENSG00000204516 MICB 8 ENSG00000204577 LILRB3 8 ENSG00000204947ZNF425 8 ENSG00000205269 TMEM170B 8 ENSG00000205744 DENND1C 8ENSG00000211689 TRGC1 8 ENSG00000213203 GIMAP1 8 ENSG00000213402 PTPRCAP8 ENSG00000213445 SIPA1 8 ENSG00000213654 GPSM3 8 ENSG00000213658 LAT 8ENSG00000213809 KLRK1 8 ENSG00000215114 UBXN2B 8 ENSG00000216490 IFI30 8ENSG00000217128 FNIP1 8 ENSG00000217555 CKLF 8 ENSG00000224397 8ENSG00000227191 TRGC2 8 ENSG00000227507 LTB 8 ENSG00000229164 TRAC 8ENSG00000229644 NAMPTL 8 ENSG00000235568 NFAM1 8 ENSG00000239998 LILRA28 ENSG00000241839 PLEKHO2 8 ENSG00000241878 PISD 8 ENSG00000242539 8ENSG00000244482 LILRA6 8 ENSG00000247774 PCED1B-AS1 8 ENSG00000250264 8ENSG00000255398 HCAR3 8 ENSG00000256007 ARAP1-AS1 8 ENSG00000258227CLEC5A 8 ENSG00000265206 MIR142 8 ENSG00000267121 8 ENSG00000268001 8ENSG00000269215 8 ENSG00000269728 9 ENSG00000002549 LAP3 9ENSG00000013374 NUB1 9 ENSG00000019582 CD74 9 ENSG00000026950 BTN3A1 9ENSG00000055332 EIF2AK2 9 ENSG00000059378 PARP12 9 ENSG00000067066 SP1009 ENSG00000068079 IF135 9 ENSG00000089692 LAG3 9 ENSG00000092010 PSME1 9ENSG00000100336 APOL4 9 ENSG00000100342 APOL1 9 ENSG00000100911 PSME2 9ENSG00000106785 TRIM14 9 ENSG00000107201 DDX58 9 ENSG00000111331 OAS3 9ENSG00000111335 OAS2 9 ENSG00000111801 BTN3A3 9 ENSG00000112763 BTN2A1 9ENSG00000114127 XRN1 9 ENSG00000115267 IFIH1 9 ENSG00000115415 STAT1 9ENSG00000117228 GBP1 9 ENSG00000119917 IFIT3 9 ENSG00000121858 TNFSF10 9ENSG00000123240 OPTN 9 ENSG00000123609 NMI 9 ENSG00000124201 ZNFX1 9ENSG00000124226 RNF114 9 ENSG00000124508 BTN2A2 9 ENSG00000125347 IRF1 9ENSG00000126709 IFI6 9 ENSG00000128284 APOL3 9 ENSG00000128335 APOL2 9ENSG00000130303 BST2 9 ENSG00000130487 KLHDC7B 9 ENSG00000130589 HELZ2 9ENSG00000131203 IDO1 9 ENSG00000132109 TRIM21 9 ENSG00000132274 TRIM22 9ENSG00000133106 EPSTI1 9 ENSG00000134326 CMPK2 9 ENSG00000135148 TRAFD19 ENSG00000136816 TOR1B 9 ENSG00000137628 DDX60 9 ENSG00000137959 IFI44L9 ENSG00000137965 IFI44 9 ENSG00000138496 PARP9 9 ENSG00000138642 HERC69 ENSG00000138755 CXCL9 9 ENSG00000140105 WARS 9 ENSG00000140464 PML 9ENSG00000140853 NLRC5 9 ENSG00000152778 IFIT5 9 ENSG00000156587 UBE2L6 9ENSG00000157601 MX1 9 ENSG00000158773 USF1 9 ENSG00000160710 ADAR 9ENSG00000160932 LY6E 9 ENSG00000162654 GBP4 9 ENSG00000163840 DTX3L 9ENSG00000164136 IL15 9 ENSG00000165949 IFI27 9 ENSG00000166278 C2 9ENSG00000166710 B2M 9 ENSG00000168062 BATF2 9 ENSG00000168394 TAP1 9ENSG00000168961 LGALS9 9 ENSG00000169245 CXCL10 9 ENSG00000173193 PARP149 ENSG00000173821 RNF213 9 ENSG00000177409 SAMD9L 9 ENSG00000179344HLA-DQB1 9 ENSG00000179583 CIITA 9 ENSG00000185338 SOCS1 9ENSG00000185404 SP140L 9 ENSG00000185880 TRIM69 9 ENSG00000186470 BTN3A29 ENSG00000187608 ISG15 9 ENSG00000188282 RUFY4 9 ENSG00000188313 PLSCR19 ENSG00000196126 HLA-DRB1 9 ENSG00000196735 HLA-DQA1 9 ENSG00000197142ACSL5 9 ENSG00000197536 C5orf56 9 ENSG00000204252 HLA-DOA 9ENSG00000204257 HLA-DMA 9 ENSG00000204261 TAPSAR1 9 ENSG00000204264PSMB8 9 ENSG00000204287 HLA-DRA 9 ENSG00000204525 HLA-C 9ENSG00000204592 HLA-E 9 ENSG00000204642 HLA-F 9 ENSG00000205220 PSMB10 9ENSG00000205436 EXOC3L4 9 ENSG00000206337 HCP5 9 ENSG00000206503 HLA-A 9ENSG00000213886 UBD 9 ENSG00000213928 IRF9 9 ENSG00000221963 APOL6 9ENSG00000223865 HLA-DPB1 9 ENSG00000225131 PSME2P2 9 ENSG00000225492GBP1P1 9 ENSG00000231389 HLA-DPA1 9 ENSG00000231925 TAPBP 9ENSG00000232629 HLA-DQB2 9 ENSG00000234745 HLA-B 9 ENSG00000237988OR2I1P 9 ENSG00000240065 PSMB9 9 ENSG00000242574 HLA-DMB 9ENSG00000263013 9 ENSG00000269640 10 ENSG00000167535 CACNB3 10ENSG00000109339 MAPK10

TABLE 14 22 genes that were selected from the 3,936 to predict themolecular subtypes in the Validation Cohort (endobronchial biopsies)Gene Module Gene Name EnsemblID 1 PHLDB1 ENSG00000019144 1 MARVELD1ENSG00000155254 1 KIRREL1 ENSG00000183853 2 CCNL2 ENSG00000221978 2MSANTD2 ENSG00000120458 2 LUC7L ENSG00000007392 3 BTG2 ENSG00000159388 3ZFP36 ENSG00000128016 4 COX6A1 ENSG00000111775 4 COX7A2 ENSG000001126955 RACGAP1 ENSG00000161800 5 TPX2 ENSG00000088325 6 NEK11 ENSG000001146706 IFT88 ENSG00000032742 7 RPL26 ENSG00000161970 7 RPL23 ENSG000001256918 DOCK2 ENSG00000134516 8 CD53 ENSG00000143119 8 LAPTM5 ENSG000001625119 UBE2L6 ENSG00000156587 9 EPSTI1 ENSG00000133106 9 TAP1 ENSG00000168394

TABLE 15 8 genes that were selected out of the 22 genes (Table 14) topredict the Proliferative subtype or not in the bronchial brushes GeneModule Gene Name EnsemblID 4 COX6A1 ENSG00000111775 4 COX7A2ENSG00000112695 5 RACGAP1 ENSG00000161800 5 TPX2 ENSG00000088325 6 NEK11ENSG00000114670 6 IFT88 ENSG00000032742 7 RPL26 ENSG00000161970 7 RPL23ENSG00000125691

TABLE 16 112 genes used to predict progression/persistence versusregression in endobronchial biopsies classified to be in theProliferative subtype. Genes in Module 9 associated withprogression/regression. These genes are contained within Table 13.EnsemblID GeneSymbols ENSG00000002549 LAP3 ENSG00000013374 NUB1ENSG00000019582 CD74 ENSG00000026950 BTN3A1 ENSG00000055332 EIF2AK2ENSG00000059378 PARP12 ENSG00000067066 SP100 ENSG00000068079 IFI35ENSG00000089692 LAG3 ENSG00000092010 PSME1 ENSG00000100336 APOL4ENSG00000100342 APOL1 ENSG00000100911 PSME2 ENSG00000106785 TRIM14ENSG00000107201 DDX58 ENSG00000111331 OAS3 ENSG00000111335 OAS2ENSG00000111801 BTN3A3 ENSG00000112763 BTN2A1 ENSG00000114127 XRN1ENSG00000115267 IFIH1 ENSG00000115415 STAT1 ENSG00000117228 GBP1ENSG00000119917 IFIT3 ENSG00000121858 TNFSF10 ENSG00000123240 OPTNENSG00000123609 NMI ENSG00000124201 ZNFX1 ENSG00000124226 RNF114ENSG00000124508 BTN2A2 ENSG00000125347 IRF1 ENSG00000126709 IFI6ENSG00000128284 APOL3 ENSG00000128335 APOL2 ENSG00000130303 BST2ENSG00000130487 KLHDC7B ENSG00000130589 HELZ2 ENSG00000131203 IDO1ENSG00000132109 TRIM21 ENSG00000132274 TRIM22 ENSG00000133106 EPSTI1ENSG00000134326 CMPK2 ENSG00000135148 TRAFD1 ENSG00000136816 TOR1BENSG00000137628 DDX60 ENSG00000137959 IFI44L ENSG00000137965 IFI44ENSG00000138496 PARP9 ENSG00000138642 HERC6 ENSG00000138755 CXCL9ENSG00000140105 WARS ENSG00000140464 PML ENSG00000140853 NLRC5ENSG00000152778 IFIT5 ENSG00000156587 UBE2L6 ENSG00000157601 MX1ENSG00000158773 USF1 ENSG00000160710 ADAR ENSG00000160932 LY6EENSG00000162654 GBP4 ENSG00000163840 DTX3L ENSG00000164136 IL15ENSG00000165949 IFI27 ENSG00000166278 C2 ENSG00000166710 B2MENSG00000168062 BATF2 ENSG00000168394 TAP1 ENSG00000168961 LGALS9ENSG00000169245 CXCL10 ENSG00000173193 PARP14 ENSG00000173821 RNF213ENSG00000177409 SAMD9L ENSG00000179344 HLA-DQB1 ENSG00000179583 CIITAENSG00000185338 SOCS1 ENSG00000185404 SP140L ENSG00000185880 TRIM69ENSG00000186470 BTN3A2 ENSG00000187608 ISG15 ENSG00000188282 RUFY4ENSG00000188313 PLSCR1 ENSG00000196126 HLA-DRB1 ENSG00000196735 HLA-DQA1ENSG00000197142 ACSL5 ENSG00000197536 C5orf56 ENSG00000204252 HLA-DOAENSG00000204257 HLA-DMA ENSG00000204261 TAPSAR1 ENSG00000204264 PSMB8ENSG00000204287 HLA-DRA ENSG00000204525 HLA-C ENSG00000204592 HLA-EENSG00000204642 HLA-F ENSG00000205220 PSMB10 ENSG00000205436 EXOC3L4ENSG00000206337 HCP5 ENSG00000206503 HLA-A ENSG00000213886 UBDENSG00000213928 IRF9 ENSG00000221963 APOL6 ENSG00000223865 HLA-DPB1ENSG00000225131 PSME2P2 ENSG00000225492 GBP1P1 ENSG00000231389 HLA-DPA1ENSG00000231925 TAPBP ENSG00000232629 HLA-DQB2 ENSG00000234745 HLA-BENSG00000237988 OR2I1P ENSG00000240065 PSMB9 ENSG00000242574 HLA-DMBENSG00000263013 RP11-876N24.5 ENSG00000269640

The methods described herein relate to the determination of theexpression level of at least one gene. In some embodiments of any of theaspects, the at least one gene can be one or more genes selected fromTables 13, 14, 15, and/or 16. In some embodiments of any of the aspects,the gene lists of Tables 13, 14 and 16 are relevant to endobronchialbiopsy samples that range in histology from normal to premalignant. Insome embodiments of any of the aspects, where the sample is anendobronchial biopsy sample, the one or more genes are selected fromTable 13, 14 and/or 16. In some embodiments of any of the aspects, Table15 is relevant for normal bronchial brushings. In some embodiments ofany of the aspects, where the sample is bronchial brushing sample (e.g,of normal tissue), the one or more genes are selected from Table 15.

In some embodiments of any of the aspects, the one or more genesselected from Table 13 or 16 are not B2M, HLA-DRA, HLA-DRB1, orHLA-DPA1. In some embodiments of any of the aspects, if the one or moregenes selected from Table 13 or 16 include B2M, HLA-DRA, HLA-DRB1,and/or HLA-DPA1, at least one additional gene from Table 13 or 16 isselected.

For convenience, the meaning of some terms and phrases used in thespecification, examples, and appended claims, are provided below. Unlessstated otherwise, or implicit from context, the following terms andphrases include the meanings provided below. The definitions areprovided to aid in describing particular embodiments, and are notintended to limit the claimed invention, because the scope of theinvention is limited only by the claims. Unless otherwise defined, alltechnical and scientific terms used herein have the same meaning ascommonly understood by one of ordinary skill in the art to which thisinvention belongs. If there is an apparent discrepancy between the usageof a term in the art and its definition provided herein, the definitionprovided within the specification shall prevail.

For convenience, certain terms employed herein, in the specification,examples and appended claims are collected here.

As used herein, the term “cancer” relates generally to a class ofdiseases or conditions in which abnormal cells divide without controland can invade nearby tissues. Cancer cells can also spread to otherparts of the body through the blood and lymph systems. There are severalmain types of cancer. Carcinoma is a cancer that begins in the skin orin tissues that line or cover internal organs. Sarcoma is a cancer thatbegins in bone, cartilage, fat, muscle, blood vessels, or otherconnective or supportive tissue. Leukemia is a cancer that starts inblood-forming tissue such as the bone marrow, and causes large numbersof abnormal blood cells to be produced and enter the blood. Lymphoma andmultiple myeloma are cancers that begin in the cells of the immunesystem. Central nervous system cancers are cancers that begin in thetissues of the brain and spinal cord.

In some embodiments of any of the aspects, the cancer is a primarycancer. In some embodiments of any of the aspects, the cancer is amalignant cancer. As used herein, the term “malignant” refers to acancer in which a group of tumor cells display one or more ofuncontrolled growth (i.e., division beyond normal limits), invasion(i.e., intrusion on and destruction of adjacent tissues), and metastasis(i.e., spread to other locations in the body via lymph or blood). Asused herein, the term “metastasize” refers to the spread of cancer fromone part of the body to another. A tumor formed by cells that havespread is called a “metastatic tumor” or a “metastasis.” The metastatictumor contains cells that are like those in the original (primary)tumor. As used herein, the term “benign” or “non-malignant” refers totumors that may grow larger but do not spread to other parts of thebody. Benign tumors are self-limited and typically do not invade ormetastasize.

A “cancer cell” or “tumor cell” refers to an individual cell of acancerous growth or tissue. A tumor refers generally to a swelling orlesion formed by an abnormal growth of cells, which may be benign,pre-malignant, or malignant. Most cancer cells form tumors, but some,e.g., leukemia, do not necessarily form tumors. For those cancer cellsthat form tumors, the terms cancer (cell) and tumor (cell) are usedinterchangeably.

As used herein the term “neoplasm” refers to any new and abnormal growthof tissue, e.g., an abnormal mass of tissue, the growth of which exceedsand is uncoordinated with that of the normal tissues. Thus, a neoplasmcan be a benign neoplasm, premalignant neoplasm, or a malignantneoplasm.

A subject that has a cancer or a tumor is a subject having objectivelymeasurable cancer cells present in the subject's body. Included in thisdefinition are malignant, actively proliferative cancers, as well aspotentially dormant tumors or micrometastatses. Cancers which migratefrom their original location and seed other vital organs can eventuallylead to the death of the subject through the functional deterioration ofthe affected organs.

Examples of cancer include but are not limited to, carcinoma, lymphoma,blastoma, sarcoma, leukemia, basal cell carcinoma, biliary tract cancer;bladder cancer; bone cancer; brain and CNS cancer; breast cancer; cancerof the peritoneum; cervical cancer; choriocarcinoma; colon and rectumcancer; connective tissue cancer; cancer of the digestive system;endometrial cancer; esophageal cancer; eye cancer; cancer of the headand neck; gastric cancer (including gastrointestinal cancer);glioblastoma (GBM); hepatic carcinoma; hepatoma; intra-epithelialneoplasm.; kidney or renal cancer; larynx cancer; leukemia; livercancer; lung cancer (e.g., small-cell lung cancer, non-small cell lungcancer, adenocarcinoma of the lung, and squamous carcinoma of the lung);lymphoma including Hodgkin's and non-Hodgkin's lymphoma; melanoma;myeloma; neuroblastoma; oral cavity cancer (e.g., lip, tongue, mouth,and pharynx); ovarian cancer; pancreatic cancer; prostate cancer;retinoblastoma; rhabdomyosarcoma; rectal cancer; cancer of therespiratory system; salivary gland carcinoma; sarcoma; skin cancer;squamous cell cancer; stomach cancer; testicular cancer; thyroid cancer;uterine or endometrial cancer; cancer of the urinary system; vulvalcancer; as well as other carcinomas and sarcomas; as well as B-celllymphoma (including low grade/follicular non-Hodgkin's lymphoma (NHL);small lymphocytic (SL) NHL; intermediate grade/follicular NHL;intermediate grade diffuse NHL; high grade immunoblastic NHL; high gradelymphoblastic NHL; high grade small non-cleaved cell NHL; bulky diseaseNHL; mantle cell lymphoma; AIDS-related lymphoma; and Waldenstrom'sMacroglobulinemia); chronic lymphocytic leukemia (CLL); acutelymphoblastic leukemia (ALL); Hairy cell leukemia; chronic myeloblasticleukemia; and post-transplant lymphoproliferative disorder (PTLD), aswell as abnormal vascular proliferation associated with phakomatoses,edema (such as that associated with brain tumors), and Meigs' syndrome

A “cancer cell” is a cancerous, pre-cancerous, or transformed cell,either in vivo, ex vivo, or in tissue culture, that has spontaneous orinduced phenotypic changes that do not necessarily involve the uptake ofnew genetic material. Although transformation can arise from infectionwith a transforming virus and incorporation of new genomic nucleic acid,or uptake of exogenous nucleic acid, it can also arise spontaneously orfollowing exposure to a carcinogen, thereby mutating an endogenous gene.Transformation/cancer is associated with, e.g., morphological changes,immortalization of cells, aberrant growth control, foci formation,anchorage independence, malignancy, loss of contact inhibition anddensity limitation of growth, growth factor or serum independence, tumorspecific markers, invasiveness or metastasis, and tumor growth insuitable animal hosts such as nude mice.

The terms “decrease”, “reduced”, “reduction”, or “inhibit” are all usedherein to mean a decrease by a statistically significant amount. In someembodiments, “reduce,” “reduction” or “decrease” or “inhibit” typicallymeans a decrease by at least 10% as compared to a reference level (e.g.the absence of a given treatment or agent) and can include, for example,a decrease by at least about 10%, at least about 20%, at least about25%, at least about 30%, at least about 35%, at least about 40%, atleast about 45%, at least about 50%, at least about 55%, at least about60%, at least about 65%, at least about 70%, at least about 75%, atleast about 80%, at least about 85%, at least about 90%, at least about95%, at least about 98%, at least about 99%, or more. As used herein,“reduction” or “inhibition” does not encompass a complete inhibition orreduction as compared to a reference level. “Complete inhibition” is a100% inhibition as compared to a reference level. A decrease can bepreferably down to a level accepted as within the range of normal for anindividual without a given disorder.

The terms “increased”, “increase”, “enhance”, or “activate” are all usedherein to mean an increase by a statically significant amount. In someembodiments, the terms “increased”, “increase”, “enhance”, or “activate”can mean an increase of at least 10% as compared to a reference level,for example an increase of at least about 20%, or at least about 30%, orat least about 40%, or at least about 50%, or at least about 60%, or atleast about 70%, or at least about 80%, or at least about 90% or up toand including a 100% increase or any increase between 10-100% ascompared to a reference level, or at least about a 2-fold, or at leastabout a 3-fold, or at least about a 4-fold, or at least about a 5-foldor at least about a 10-fold increase, or any increase between 2-fold and10-fold or greater as compared to a reference level. In the context of amarker or symptom, a “increase” is a statistically significant increasein such level.

As used herein, a “subject” means a human or animal. Usually the animalis a vertebrate such as a primate, rodent, domestic animal or gameanimal. Primates include chimpanzees, cynomologous monkeys, spidermonkeys, and macaques, e.g., Rhesus. Rodents include mice, rats,woodchucks, ferrets, rabbits and hamsters. Domestic and game animalsinclude cows, horses, pigs, deer, bison, buffalo, feline species, e.g.,domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g.,chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. Insome embodiments, the subject is a mammal, e.g., a primate, e.g., ahuman. The terms, “individual,” “patient” and “subject” are usedinterchangeably herein.

Preferably, the subject is a mammal. The mammal can be a human,non-human primate, mouse, rat, dog, cat, horse, or cow, but is notlimited to these examples. Mammals other than humans can beadvantageously used as subjects that represent animal models ofbronchial premalignant lesions. A subject can be male or female.

A subject can be one who has been previously diagnosed with oridentified as suffering from or having a condition in need of treatment(e.g. bronchial premalignant lesions) or one or more complicationsrelated to such a condition, and optionally, have already undergonetreatment for bronchial premalignant lesions or the one or morecomplications related to bronchial premalignant lesions. Alternatively,a subject can also be one who has not been previously diagnosed ashaving bronchial premalignant lesions or one or more complicationsrelated to bronchial premalignant lesions. For example, a subject can beone who exhibits one or more risk factors for bronchial premalignantlesions or one or more complications related to bronchial premalignantlesions or a subject who does not exhibit risk factors.

A “subject in need” of treatment for a particular condition can be asubject having that condition, diagnosed as having that condition, or atrisk of developing that condition.

As used herein, the terms “protein” and “polypeptide” are usedinterchangeably herein to designate a series of amino acid residues,connected to each other by peptide bonds between the alpha-amino andcarboxy groups of adjacent residues. The terms “protein”, and“polypeptide” refer to a polymer of amino acids, including modifiedamino acids (e.g., phosphorylated, glycated, glycosylated, etc.) andamino acid analogs, regardless of its size or function. “Protein” and“polypeptide” are often used in reference to relatively largepolypeptides, whereas the term “peptide” is often used in reference tosmall polypeptides, but usage of these terms in the art overlaps. Theterms “protein” and “polypeptide” are used interchangeably herein whenreferring to a gene product and fragments thereof. Thus, exemplarypolypeptides or proteins include gene products, naturally occurringproteins, homologs, orthologs, paralogs, fragments and otherequivalents, variants, fragments, and analogs of the foregoing.

In the various embodiments described herein, it is further contemplatedthat variants (naturally occurring or otherwise), alleles, homologs,conservatively modified variants, and/or conservative substitutionvariants of any of the particular polypeptides described areencompassed. As to amino acid sequences, one of skill will recognizethat individual substitutions, deletions or additions to a nucleic acid,peptide, polypeptide, or protein sequence which alters a single aminoacid or a small percentage of amino acids in the encoded sequence is a“conservatively modified variant” where the alteration results in thesubstitution of an amino acid with a chemically similar amino acid andretains the desired activity of the polypeptide. Such conservativelymodified variants are in addition to and do not exclude polymorphicvariants, interspecies homologs, and alleles consistent with thedisclosure.

A given amino acid can be replaced by a residue having similarphysiochemical characteristics, e.g., substituting one aliphatic residuefor another (such as Ile, Val, Leu, or Ala for one another), orsubstitution of one polar residue for another (such as between Lys andArg; Glu and Asp; or Gln and Asn). Other such conservativesubstitutions, e.g., substitutions of entire regions having similarhydrophobicity characteristics, are well known. Polypeptides comprisingconservative amino acid substitutions can be tested in any one of theassays described herein to confirm that a desired activity, e.g.activity and specificity of a native or reference polypeptide isretained.

Amino acids can be grouped according to similarities in the propertiesof their side chains (in A. L. Lehninger, in Biochemistry, second ed.,pp. 73-75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A),Val (V), Leu (L), Ile (I), Pro (P), Phe (F), Trp (W), Met (M); (2)uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N),Gln (Q); (3) acidic: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His(H). Alternatively, naturally occurring residues can be divided intogroups based on common side-chain properties: (1) hydrophobic:Norleucine, Met, Ala, Val, Leu, Ile; (2) neutral hydrophilic: Cys, Ser,Thr, Asn, Gln; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5)residues that influence chain orientation: Gly, Pro; (6) aromatic: Trp,Tyr, Phe. Non-conservative substitutions will entail exchanging a memberof one of these classes for another class. Particular conservativesubstitutions include, for example; Ala into Gly or into Ser; Arg intoLys; Asn into Gln or into His; Asp into Glu; Cys into Ser; Gln into Asn;Glu into Asp; Gly into Ala or into Pro; His into Asn or into Gln; Ileinto Leu or into Val; Leu into Ile or into Val; Lys into Arg, into Glnor into Glu; Met into Leu, into Tyr or into Ile; Phe into Met, into Leuor into Tyr; Ser into Thr; Thr into Ser; Trp into Tyr; Tyr into Trp;and/or Phe into Val, into Ile or into Leu.

In some embodiments, the polypeptide described herein (or a nucleic acidencoding such a polypeptide) can be a functional fragment of one of theamino acid sequences described herein. As used herein, a “functionalfragment” is a fragment or segment of a peptide which retains at least50% of the wildtype reference polypeptide's activity according to theassays described below herein. A functional fragment can compriseconservative substitutions of the sequences disclosed herein.

In some embodiments, the polypeptide described herein can be a variantof a sequence described herein. In some embodiments, the variant is aconservatively modified variant. Conservative substitution variants canbe obtained by mutations of native nucleotide sequences, for example. A“variant,” as referred to herein, is a polypeptide substantiallyhomologous to a native or reference polypeptide, but which has an aminoacid sequence different from that of the native or reference polypeptidebecause of one or a plurality of deletions, insertions or substitutions.Variant polypeptide-encoding DNA sequences encompass sequences thatcomprise one or more additions, deletions, or substitutions ofnucleotides when compared to a native or reference DNA sequence, butthat encode a variant protein or fragment thereof that retains activity.A wide variety of PCR-based site-specific mutagenesis approaches areknown in the art and can be applied by the ordinarily skilled artisan.

A variant amino acid or DNA sequence can be at least 90%, at least 91%,at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, atleast 97%, at least 98%, at least 99%, or more, identical to a native orreference sequence. The degree of homology (percent identity) between anative and a mutant sequence can be determined, for example, bycomparing the two sequences using freely available computer programscommonly employed for this purpose on the world wide web (e.g. BLASTp orBLASTn with default settings).

Alterations of the native amino acid sequence can be accomplished by anyof a number of techniques known to one of skill in the art. Mutationscan be introduced, for example, at particular loci by synthesizingoligonucleotides containing a mutant sequence, flanked by restrictionsites enabling ligation to fragments of the native sequence. Followingligation, the resulting reconstructed sequence encodes an analog havingthe desired amino acid insertion, substitution, or deletion.Alternatively, oligonucleotide-directed site-specific mutagenesisprocedures can be employed to provide an altered nucleotide sequencehaving particular codons altered according to the substitution,deletion, or insertion required. Techniques for making such alterationsare very well established and include, for example, those disclosed byWalder et al. (Gene 42:133, 1986); Bauer et al. (Gene 37:73, 1985);Craik (BioTechniques, January 1985, 12-19); Smith et al. (GeneticEngineering: Principles and Methods, Plenum Press, 1981); and U.S. Pat.Nos. 4,518,584 and 4,737,462, which are herein incorporated by referencein their entireties. Any cysteine residue not involved in maintainingthe proper conformation of the polypeptide also can be substituted,generally with serine, to improve the oxidative stability of themolecule and prevent aberrant crosslinking. Conversely, cysteine bond(s)can be added to the polypeptide to improve its stability or facilitateoligomerization.

As used herein, the term “nucleic acid” or “nucleic acid sequence”refers to any molecule, preferably a polymeric molecule, incorporatingunits of ribonucleic acid, deoxyribonucleic acid or an analog thereof.The nucleic acid can be either single-stranded or double-stranded. Asingle-stranded nucleic acid can be one nucleic acid strand of adenatured double-stranded DNA. Alternatively, it can be asingle-stranded nucleic acid not derived from any double-stranded DNA.In one aspect, the nucleic acid can be DNA. In another aspect, thenucleic acid can be RNA. Suitable DNA can include, e.g., genomic DNA orcDNA. Suitable RNA can include, e.g., mRNA.

The term “expression” refers to the cellular processes involved inproducing RNA and proteins and as appropriate, secreting proteins,including where applicable, but not limited to, for example,transcription, transcript processing, translation and protein folding,modification and processing. Expression can refer to the transcriptionand stable accumulation of sense (mRNA) or antisense RNA derived from anucleic acid fragment or fragments of the invention and/or to thetranslation of mRNA into a polypeptide.

In some embodiments, the expression of a biomarker(s), target(s), orgene/polypeptide described herein is/are tissue-specific. In someembodiments, the expression of a biomarker(s), target(s), orgene/polypeptide described herein is/are global. In some embodiments,the expression of a biomarker(s), target(s), or gene/polypeptidedescribed herein is systemic.

“Expression products” include RNA transcribed from a gene, andpolypeptides obtained by translation of mRNA transcribed from a gene.The term “gene” means the nucleic acid sequence which is transcribed(DNA) to RNA in vitro or in vivo when operably linked to appropriateregulatory sequences. The gene may or may not include regions precedingand following the coding region, e.g. 5′ untranslated (5′UTR) or“leader” sequences and 3′ UTR or “trailer” sequences, as well asintervening sequences (introns) between individual coding segments(exons).

“Marker” in the context of the present invention refers to an expressionproduct, e.g., nucleic acid or polypeptide which is differentiallypresent in a sample taken from subjects having bronchial premalignantlesions of a particular subtype, as compared to a comparable sampletaken from control subjects (e.g., a healthy subject). The term“biomarker” is used interchangeably with the term “marker.”

In some embodiments, the methods described herein relate to measuring,detecting, or determining the level of at least one marker. As usedherein, the term “detecting” or “measuring” refers to observing a signalfrom, e.g. a probe, label, or target molecule to indicate the presenceof an analyte in a sample. Any method known in the art for detecting aparticular label moiety can be used for detection. Exemplary detectionmethods include, but are not limited to, spectroscopic, fluorescent,photochemical, biochemical, immunochemical, electrical, optical orchemical methods. In some embodiments of any of the aspects, measuringcan be a quantitative observation.

As used herein, the terms “treat,” “treatment,” “treating,” or“amelioration” refer to therapeutic treatments, wherein the object is toreverse, alleviate, ameliorate, inhibit, slow down or stop theprogression or severity of a condition associated with a disease ordisorder, e.g. bronchial premalignant lesion. The term “treating”includes reducing or alleviating at least one adverse effect or symptomof a condition, disease or disorder associated with a bronchialpremalignant lesion. Treatment is generally “effective” if one or moresymptoms or clinical markers are reduced. Alternatively, treatment is“effective” if the progression of a disease is reduced or halted. Thatis, “treatment” includes not just the improvement of symptoms ormarkers, but also a cessation of, or at least slowing of, progress orworsening of symptoms compared to what would be expected in the absenceof treatment. Beneficial or desired clinical results include, but arenot limited to, alleviation of one or more symptom(s), diminishment ofextent of disease, stabilized (i.e., not worsening) state of disease,delay or slowing of disease progression, amelioration or palliation ofthe disease state, remission (whether partial or total), and/ordecreased mortality, whether detectable or undetectable. The term“treatment” of a disease also includes providing relief from thesymptoms or side-effects of the disease (including palliativetreatment).

As used herein, the term “pharmaceutical composition” refers to theactive agent in combination with a pharmaceutically acceptable carriere.g. a carrier commonly used in the pharmaceutical industry. The phrase“pharmaceutically acceptable” is employed herein to refer to thosecompounds, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio. In some embodimentsof any of the aspects, a pharmaceutically acceptable carrier can be acarrier other than water. In some embodiments of any of the aspects, apharmaceutically acceptable carrier can be a cream, emulsion, gel,liposome, nanoparticle, and/or ointment. In some embodiments of any ofthe aspects, a pharmaceutically acceptable carrier can be an artificialor engineered carrier, e.g., a carrier that the active ingredient wouldnot be found to occur in in nature.

As used herein, the term “administering,” refers to the placement of acompound as disclosed herein into a subject by a method or route whichresults in at least partial delivery of the agent at a desired site.Pharmaceutical compositions comprising the compounds disclosed hereincan be administered by any appropriate route which results in aneffective treatment in the subject. In some embodiments, administrationcomprises physical human activity, e.g., an injection, act of ingestion,an act of application, and/or manipulation of a delivery device ormachine. Such activity can be performed, e.g., by a medical professionaland/or the subject being treated.

As used herein, “contacting” refers to any suitable means fordelivering, or exposing, an agent to at least one cell. Exemplarydelivery methods include, but are not limited to, direct delivery tocell culture medium, perfusion, injection, or other delivery method wellknown to one skilled in the art. In some embodiments, contactingcomprises physical human activity, e.g., an injection; an act ofdispensing, mixing, and/or decanting; and/or manipulation of a deliverydevice or machine.

As used herein, the term “inhibitor” refers to an agent which candecrease the expression and/or activity of the target molecule oractivity or process, e.g. by at least 10% or more, e.g. by 10% or more,50% or more, 70% or more, 80% or more, 90% or more, 95% or more, or 98%or more.

As used herein, the terms “drug”, “compound” or “agent” are usedinterchangeably and refer to molecules and/or compositions. Thecompounds/agents include, but are not limited to, chemical compounds andmixtures of chemical compounds, e.g., small organic or inorganicmolecules; saccharines; oligosaccharides; polysaccharides; biologicalmacromolecules, e.g., peptides, proteins, and peptide analogs andderivatives; peptidomimetics; nucleic acids; nucleic acid analogs andderivatives; extracts made from biological materials such as bacteria,plants, fungi, or animal cells or tissues; naturally occurring orsynthetic compositions; peptides; aptamers; and antibodies andintrabodies, or fragments thereof. In some embodiments, “drug” as usedherein refers to an agent approved for medical use, e.g., by the FDA.

The term “statistically significant” or “significantly” refers tostatistical significance and generally means a two standard deviation(2SD) or greater difference.

Other than in the operating examples, or where otherwise indicated, allnumbers expressing quantities of ingredients or reaction conditions usedherein should be understood as modified in all instances by the term“about.” The term “about” when used in connection with percentages canmean±1%.

As used herein, the term “comprising” means that other elements can alsobe present in addition to the defined elements presented. The use of“comprising” indicates inclusion rather than limitation.

The term “consisting of” refers to compositions, methods, and respectivecomponents thereof as described herein, which are exclusive of anyelement not recited in that description of the embodiment.

As used herein the term “consisting essentially of” refers to thoseelements required for a given embodiment. The term permits the presenceof additional elements that do not materially affect the basic and novelor functional characteristic(s) of that embodiment of the invention.

The singular terms “a,” “an,” and “the” include plural referents unlesscontext clearly indicates otherwise. Similarly, the word “or” isintended to include “and” unless the context clearly indicatesotherwise. Although methods and materials similar or equivalent to thosedescribed herein can be used in the practice or testing of thisdisclosure, suitable methods and materials are described below. Theabbreviation, “e.g.” is derived from the Latin exempli gratia, and isused herein to indicate a non-limiting example. Thus, the abbreviation“e.g.” is synonymous with the term “for example.”

Groupings of alternative elements or embodiments of the inventiondisclosed herein are not to be construed as limitations. Each groupmember can be referred to and claimed individually or in any combinationwith other members of the group or other elements found herein. One ormore members of a group can be included in, or deleted from, a group forreasons of convenience and/or patentability. When any such inclusion ordeletion occurs, the specification is herein deemed to contain the groupas modified thus fulfilling the written description of all Markushgroups used in the appended claims.

Unless otherwise defined herein, scientific and technical terms used inconnection with the present application shall have the meanings that arecommonly understood by those of ordinary skill in the art to which thisdisclosure belongs. It should be understood that this invention is notlimited to the particular methodology, protocols, and reagents, etc.,described herein and as such can vary. The terminology used herein isfor the purpose of describing particular embodiments only, and is notintended to limit the scope of the present invention, which is definedsolely by the claims. Definitions of common terms in immunology andmolecular biology can be found in The Merck Manual of Diagnosis andTherapy, 20th Edition, published by Merck Sharp & Dohme Corp., 2018(ISBN 0911910190, 978-0911910421); Robert S. Porter et al. (eds.), TheEncyclopedia of Molecular Cell Biology and Molecular Medicine, publishedby Blackwell Science Ltd., 1999-2012 (ISBN 9783527600908); and Robert A.Meyers (ed.), Molecular Biology and Biotechnology: a Comprehensive DeskReference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8);Immunology by Werner Luttmann, published by Elsevier, 2006; Janeway'sImmunobiology, Kenneth Murphy, Allan Mowat, Casey Weaver (eds.), W. W.Norton & Company, 2016 (ISBN 0815345054, 978-0815345053); Lewin's GenesXI, published by Jones & Bartlett Publishers, 2014 (ISBN-1449659055);Michael Richard Green and Joseph Sambrook, Molecular Cloning: ALaboratory Manual, 4th ed., Cold Spring Harbor Laboratory Press, ColdSpring Harbor, N.Y., USA (2012) (ISBN 1936113414); Davis et al., BasicMethods in Molecular Biology, Elsevier Science Publishing, Inc., NewYork, USA (2012) (ISBN 044460149X); Laboratory Methods in Enzymology:DNA, Jon Lorsch (ed.) Elsevier, 2013 (ISBN 0124199542); CurrentProtocols in Molecular Biology (CPMB), Frederick M. Ausubel (ed.), JohnWiley and Sons, 2014 (ISBN 047150338X, 9780471503385), Current Protocolsin Protein Science (CPPS), John E. Coligan (ed.), John Wiley and Sons,Inc., 2005; and Current Protocols in Immunology (CPI) (John E. Coligan,ADA M Kruisbeek, David H Margulies, Ethan M Shevach, Warren Strobe,(eds.) John Wiley and Sons, Inc., 2003 (ISBN 0471142735, 9780471142737),the contents of which are all incorporated by reference herein in theirentireties.

Other terms are defined herein within the description of the variousaspects of the invention.

All patents and other publications; including literature references,issued patents, published patent applications, and co-pending patentapplications; cited throughout this application are expresslyincorporated herein by reference for the purpose of describing anddisclosing, for example, the methodologies described in suchpublications that might be used in connection with the technologydescribed herein. These publications are provided solely for theirdisclosure prior to the filing date of the present application. Nothingin this regard should be construed as an admission that the inventorsare not entitled to antedate such disclosure by virtue of priorinvention or for any other reason. All statements as to the date orrepresentation as to the contents of these documents is based on theinformation available to the applicants and does not constitute anyadmission as to the correctness of the dates or contents of thesedocuments.

The description of embodiments of the disclosure is not intended to beexhaustive or to limit the disclosure to the precise form disclosed.While specific embodiments of, and examples for, the disclosure aredescribed herein for illustrative purposes, various equivalentmodifications are possible within the scope of the disclosure, as thoseskilled in the relevant art will recognize. For example, while methodsteps or functions are presented in a given order, alternativeembodiments may perform functions in a different order, or functions maybe performed substantially concurrently. The teachings of the disclosureprovided herein can be applied to other procedures or methods asappropriate. The various embodiments described herein can be combined toprovide further embodiments. Aspects of the disclosure can be modified,if necessary, to employ the compositions, functions and concepts of theabove references and application to provide yet further embodiments ofthe disclosure. These and other changes can be made to the disclosure inlight of the detailed description. All such modifications are intendedto be included within the scope of the appended claims.

Specific elements of any of the foregoing embodiments can be combined orsubstituted for elements in other embodiments. Furthermore, whileadvantages associated with certain embodiments of the disclosure havebeen described in the context of these embodiments, other embodimentsmay also exhibit such advantages, and not all embodiments neednecessarily exhibit such advantages to fall within the scope of thedisclosure.

The technology described herein is further illustrated by the followingexamples which in no way should be construed as being further limiting.

Some embodiments of the technology described herein can be definedaccording to any of the following numbered paragraphs:

-   -   1. A method of treating bronchial premalignant lesions, the        method comprising:        -   administering at least one of:            -   i. both a bronchoscopy-based procedure to survey the                central airway and a chest CT scan;            -   ii. at least every 6 months, one of a bronchoscopy-based                procedure to survey the central airway and a chest CT                scan; and/or            -   iii. at least one anti-proliferative drug;        -   to a subject determined to have at least one of:        -   an increased level of expression of at least one module 5            gene as compared to a non-proliferative lesion reference            level; and        -   a decreased level of expression of at least one module 6            gene as compared to a non-proliferative lesion reference            level.    -   2. The method of paragraph 1, wherein the at least one module 5        gene is selected from the group consisting of:        -   RACGAP1 and TPX2; and    -   the at least one module 6 gene is selected from the group        consisting of:        -   NEK11 and IFT88.    -   3. The method of any of paragraphs 1-2, wherein the subject is        further determined to have an increased level of expression of        at least one module 7 or module 4 gene.    -   4. The method of paragraph 3, wherein the at least one module 7        or module 4 gene is selected from the group consisting of:        -   COX6A1; COX7A2; RPL26; and RPL23.    -   5. The method of any of paragraphs 1-4, wherein the level of        expression of each of the genes of Table 15 is determined.    -   6. The method of any of paragraphs 1-5, wherein the at least one        anti-proliferative drug is selected from the group consisting        of:        -   Acetylcholine receptor antagonist; Acetylcholinesterase            inhibitors; Adenosine receptor antagonists; Adrenergic            receptor antagonists; AKT inhibitors; Angiotensin receptor            antagonists; Apoptosis stimulants; Aurora kinase inhibitors;            CDK inhibitors; Cyclooxygenase inhibitors; Cytokine            production inhibitors; Dehydrogenase inhibitors; DNA protein            kinase inhibitors; focal adhesion inhibitors; Dopamine            receptor antagonist; EGFR inhibitors; ERK1 and ERK2            phosphorylation inhibitors; Estrogen receptor agonists; EZH2            inhibitors; FLT3 inhibitors; Glucocorticoid receptor            agonists; Glutamate receptor antagonists; HDAC inhibitors;            Histamine receptor antagonists; Histone lysine            methyltransferase inhibitors; HSP inhibitors; IKK            inhibitors; Ion channel antagonists; JAK inhibitors; JNK            inhibitors; KIT inhibitors; Leucine rich repeat kinase            inhibitors; MDM inhibitors; mediator release inhibitors; MEK            inhibitors; MTOR inhibitors; Monoamine oxidase inhibitors;            NFkB pathway inhibitors; nucleophosmin inhibitors; PARP            inhibitors; PPAR receptor agonists; PI3K inhibitors;            tyrosine kinase inhibitors; Phosphodiesterase inhibitors;            protein kinase inhibitors; RAF inhibitors; RNA polymerase            inhibitors; topoisomerase inhibitors; RNA synthesis            inhibitors; SIRT inhibitors; sodium channel blockers; VEGFR            inhibitors; and Vitamin D receptor agonists.    -   7. The method of any of paragraphs 1-6, wherein the        anti-proliferative drug is administered as an inhaled        formulation or topical formulation.    -   8. The method of any of paragraphs 1-7, wherein the        anti-proliferative drug is administered during a        bronchoscopy-based procedure.    -   9. The method of any of paragraphs 1-8, wherein the        anti-proliferative drug is administered systemically.    -   10. The method of any of paragraphs 1-9, wherein the        anti-proliferative drug is administered during a        bronchoscopy-based procedure and systemically.    -   11. The method of any of paragraphs 1-10, wherein the subject is        further determined to have a decreased level of expression of at        least one module 9 gene as compared to a non-proliferative        lesion reference level and/or an increased level of expression        of at least one module 10 gene as compared to a        non-proliferative lesion reference level.    -   12. The method of paragraph 11, wherein the subject determined        to have a decreased level of expression of at least one module 9        gene and/or an increased level of expression of at least one        module 10 gene is administered at least one of:        -   i. both a bronchoscopy-based procedure to survey the central            airway wherein the lesions are biopsied to remove abnormal            tissue and a chest CT scan;        -   ii. at least every 6 months, one of a bronchoscopy-based            procedure to survey the central airway wherein the lesions            are biopsied to remove abnormal tissue and a chest CT scan;            and/or        -   iii. at least one immune stimulating drug.    -   13. A method of treating bronchial premalignant lesions, the        method comprising:        -   administering at least one of:            -   i. both a bronchoscopy-based procedure to survey the                central airway wherein the lesions are biopsied to                remove abnormal tissue and a chest CT scan;            -   ii. at least every 6 months, one of a bronchoscopy-based                procedure to survey the central airway wherein the                lesions are biopsied to remove abnormal tissue and a                chest CT scan; and/or iii. at least one immune                stimulating drug;            -   to a subject determined to have a decreased level of                expression of at least one module 9        -   gene as compared to a non-proliferative lesion reference            level and/or an increased level of expression of at least            one module 10 gene as compared to a non-proliferative lesion            reference level.    -   14. The method of any of paragraphs 11-13, wherein the module 9        gene is selected from the group consisting of:        -   EPSTI1; UBE2L6; B2M and TAP1.    -   15. The method of any of paragraphs 11-14, wherein the at least        one gene module 9 gene is selected from Table 16.    -   16. The method of any of paragraphs 11-15, wherein the module 10        gene is selected from the group consisting of:        -   CACNB3 and MAPK10.    -   17. The method of any of paragraphs 11-16, wherein the at least        one immune stimulating drug is selected from the group        consisting of:        -   immune-checkpoint inhibitors (e.g. inhibitors against, PD-1,            PD-L1, CTLA4, and LAG3); drugs that stimulate interferon            signaling (e.g. anti-viral drugs that improve interferon            signaling); DNA synthesis inhibitors; IMDH inhibitors; CDK            inhibitors; ribonucleotide reductase inhibitors;            dihydrofolate reductase inhibitors; topoisomerase            inhibitors; FLT3 inhibitors; IGF-1 inhibitors; MEK            inhibitors; aurora kinase inhibitors; PKC inhibitors; RAF            inhibitors; PDFGR/KIT inhibitors; VEGFR inhibitors; SRC            inhibitors; retinoid receptor agonists; HDAC inhibitors; DNA            methyltransferase inhibitors; and EZH2 inhibitors.    -   18. A method of treating bronchial premalignant lesions, the        method comprising:        -   administering at least one of:            -   i. both a bronchoscopy-based procedure to survey the                central airway and a chest CT scan;            -   ii. at least every 6 months, one of a bronchoscopy-based                procedure to survey the central airway and a chest CT                scan; and/or            -   iii. at least one anti-inflammatory drug;        -   to a subject determined to have at least one of:        -   an increased level of expression of at least one module 2            gene as compared to a non-inflammatory reference level; and        -   a decreased level of expression of at least one module 6            gene as compared to a non-inflammatory reference level.    -   19. The method of paragraph 17, wherein the at least one module        2 gene is selected from the group consisting of:        -   MSANTD2, CCNL2, and LUC7L; and        -   the at least one module 6 gene is selected from the group            consisting of:        -   NEK11 and IFT88.    -   20. The method of any of paragraphs 17-18, wherein the subject        is further determined to have an increased level of expression        of at least one module 7 gene, module 1 gene, or module 8 gene        and/or decreased level of expression of at least one module 4        gene or one module 5 gene.    -   21. The method of paragraph 19, wherein the at least one module        7 gene is selected from the group consisting of: RPL26 and        RPL23.    -   22. The method of paragraph 19, wherein the at least one module        1 gene is selected from the group consisting of: KIRREL; PHLDB1;        and MARVELD1.    -   23. The method of paragraph 19, wherein the at least one module        8 gene is selected from the group consisting of: DOC2; CD53; and        LAP™.    -   24. The method of paragraph 19, wherein the at least one module        4 gene is selected from the group consisting of: COX6A1 and        COX7A2    -   25. The method of paragraph 19, wherein the at least one module        5 gene is selected from the group consisting of: RACGAP1 and        TPX2    -   26. The method of any of paragraphs 17-24, wherein the level of        expression of each of the genes of Table 15 is determined.    -   27. The method of any of paragraphs 17-25, wherein the at least        one anti-inflammatory drug is selected from the group consisting        of:        -   Acetylcholine receptor antagonists; Acetylcholinesterase            inhibitors; Adenosine receptor antagonists; Adrenergic            receptor antagonists; Angiotensin receptor antagonists;            Anti-IL1B antibodies; Apoptosis stimulants; Aurora kinase            inhibitors; CDK inhibitors; Cyclooxygenase inhibitors;            Cytokine production inhibitors; Dehydrogenase inhibitors;            Dopamine receptor antagonists; EGFR inhibitors; ERK1 and            ERK2 phosphorylation inhibitors; Estrogen receptor agonists;            FLT3 inhibitors; Glucocorticoid receptor agonists; Glutamate            receptor antagonists; HDAC inhibitors; Histamine receptor            antagonists; Histone lysine methyltransferase inhibitors;            HSP inhibitors; IKK inhibitors; Ion channel antagonists; KIT            inhibitors; Leucine rich repeat kinase inhibitors; MEK            inhibitors; MDM inhibitors; Phosphodiesterase inhibitors;            Monoamine oxidase inhibitors; MTOR inhibitors; NFkB pathway            inhibitors; nucleophosmin inhibitors; PARP inhibitors; PI3K            inhibitors; PPAR receptor agonists; protein synthesis            inhibitors (e.g. chloramphenicol); RAF inhibitors; SIRT            inhibitors; Sodium channel blockers; TGF beta receptor            inhibitors; Topoisomerase inhibitors; Tyrosine kinase            inhibitors; VEGFR inhibitors; and Vitamin D receptor            agonists.    -   28. The method of any of paragraphs 17-26, wherein the        anti-inflammatory drug is administered during a        bronchoscopy-based procedure.    -   29. The method of any of paragraphs 17-27, wherein the        anti-inflammatory drug is administered systemically.    -   30. The method of any of paragraphs 17-28, wherein the        anti-inflammatory drug is administered during a        bronchoscopy-based procedure and systemically.    -   31. The method of any of paragraphs 1-29, wherein the at least        one gene is selected from Table 14.    -   32. The method of any of paragraphs 1-30, wherein the level of        expression of each of the genes of Table 14 is determined.    -   33. The method of any of paragraphs 1-31, whereby the        development of lung cancer lung squamous cell carcinoma is        prevented, delayed, or slowed.    -   34. The method of any of paragraphs 1-32, wherein the lung        cancer is lung squamous cell carcinoma.    -   35. The method of any of paragraphs 1-33, wherein the level of        expression is the level of expression in an endobronchial        biopsy, endobronchial brushing sample, large airway biopsy,        large airway brushing sample, nasal epithelial cells, sputum, or        blood obtained from the subject.    -   36. The method of any of paragraphs 1-34, wherein the level of        expression is the level of expression in a bronchial brushing        obtained from the right or left mainstem bronchus.    -   37. The method of any of paragraphs 34-35, wherein the biopsy or        brushing sample comprises morphologically-normal tissues or        cells.    -   38. The method of any of paragraphs 34-35, wherein the biopsy or        brushing sample consists of morphologically-normal tissues or        cells.    -   39. The method of any of paragraphs 1-34, wherein the level of        expression is the level of expression in a sample comprising        bronchial premalignant lesion cells.    -   40. The method of any of paragraphs 1-35, wherein the level of        expression is the level of expression in a sample comprising        morphologically-normal cells.    -   41. The method of any of the paragraphs 1-36, wherein the        subject is a smoker or former smoker.

EXAMPLES Example 1: Molecular Subtyping Reveals Immune AlterationsAssociated with Progression of Bronchial Premalignant Lesions

Described herein is the molecular characterization of bronchialpremalignant lesions and the airway field of injury identifiedepithelial and immune alterations associated with progressive/persistentbronchial dysplasia that can be leveraged to develop lung cancer riskbiomarkers and interception strategies.

Bronchial premalignant lesions (PMLs) are precursors of lung squamouscell carcinoma, but have variable outcome, and tools are lacking toidentify and treat PMLs at highest risk for progression to invasivecancer. Profiling endobronchial biopsies of PMLs obtained from high-risksmokers by RNA-Seq identified four PML subtypes with differences inepithelial and immune processes. One molecular subtype (Proliferative)is enriched with dysplastic lesions and exhibits up-regulation ofmetabolic and cell cycle pathways and down-regulation of ciliaryprocesses. RNA-Seq profiles from normal-appearing uninvolved largeairway brushings could identify subjects with Proliferative lesions withhigh specificity. Expression of interferon signaling and antigenprocessing/presentation pathways are decreased in progressive/persistentProliferative lesions and immunofluorescence indicates a depletion ofinnate and adaptive immune cells in these lesions. Molecular biomarkersmeasured in PMLs or the uninvolved airway can enhance histopathologicalgrading and indicates that immunoprevention strategies may be effectivein intercepting the progression of PMLs to lung cancer.

Introduction

Lung cancer (LC) is the leading cause of cancer death taking about160,000 U.S. lives each year, more than colorectal, pancreatic, breast,and prostate cancers combined. In order to decrease mortality,innovative strategies are needed to intercept cancer development bydiagnosing the disease at its earliest and potentially most curablestage. Recent advances based on results from the National Lung ScreeningTrial (1) are dramatically altering the landscape of early LC detectionas computed tomography (CT) screening of high-risk individualssignificantly reduces mortality. Despite this progress, biomarkers areneeded to select individuals for LC screening as eligibility criteriaaccount for less than 27% of individuals diagnosed with LC in the US (2)and to distinguish between benign or cancerous indeterminate pulmonarynodules as screening has very high false positive rate (>90%). There isalso urgent and unmet need to develop personalized therapies earlier inthe disease process to “intercept” LC prior to its development in thishigh-risk population.

Development of LC risk biomarkers and LC interception strategiesrequires a detailed understanding of the earliest molecular alterationsinvolved in lung carcinogenesis that occur in the respiratory epithelium(3, 4). Exposure to cigarette smoke creates a field of injury throughoutthe entire respiratory tract by inducing a variety of genomicalterations that can lead to an “at-risk” airway where premalignantlesions (PMLs) and LCs develop. Lung squamous cell carcinoma (LUSC)arises in the epithelial layer of the bronchial airways and is oftenpreceded by the development of PMLs through a stepwise histologicalprogression from normal epithelium to hyperplasia, squamous metaplasia,dysplasia (mild, moderate and severe), carcinoma in situ (CIS), andfinally to invasive and then metastatic LUSC (5). In fact, the presenceof high-grade persistent or progressive dysplasia (moderate or severe)is a marker of increased LC risk both at the lesion site (where they arethe presumed precursors of squamous cell lung cancer) and elsewhere inthe lung, although many dysplastic lesions do have varied outcomes (6).Currently, however, effective tools to identify PMLs are lacking athighest risk of progression to invasive carcinoma (7). The developmentof markers of disease progression would identify patients at high-risk,suggest novel lung cancer chemoprevention agents, and provide molecularbiomarkers for monitoring outcome in lung cancer prevention trials.

It is hypothesized herein that molecular characterization of bronchialbiopsies containing a mixture of epithelial and immune cells would allowus to identify transcriptomic alterations associated with high-gradehistology and premalignant lesion progression. In this study, mRNAsequencing was used to profile endobronchial biopsies and brushingsobtained through serial bronchoscopies from high-risk smokers undergoinglung cancer screening by auto-fluorescence bronchoscopy and chest CT.Using the bronchial biopsies, four molecular subtypes associated withclinical phenotypes and biological processes were identified. Onesubtype (Proliferative subtype) is enriched with biopsies havingdysplastic histology, high basal cell and low ciliated cell signals, andexpression of proliferation-associated pathways. Genes involved ininterferon signaling and T cell mediated immunity were down-regulatedamong progressive/persistent lesions within the Proliferative subtypecompared with regressive lesions and these pathways correlated withdecreases in both innate and adaptive immune cell types. Molecularclassification of biopsies into a high-grade/progressive disease groupcan be used to stratify patients into prevention trials and to monitorefficacy of the treatment. The results also indicate that personalizedlung cancer chemoprevention targeting specific cancer-related pathwaysor the immune system can have potential therapeutic benefits.

Results

Subject Population

In this study, mRNA sequencing was used to profile endobronchialbiopsies and brushings obtained through serial bronchoscopy of high-risksmokers undergoing lung cancer screening by auto-fluorescencebronchoscopy and chest CT at the Roswell Park Comprehensive CancerCenter (Roswell) in Buffalo, N.Y. The Discovery Cohort samples wereobtained from the Roswell subjects between 2010 and 2012 (DC; n=29patients, n=191 biopsies, n=91 brushes), and the Validation Cohortsamples were obtained between 2012 and 2015 (VC; n=20 patients, n=111biopsies, and 49 brushes). The subjects are predominantly older smokers,many of which have a history of lung cancer, chronic obstructivepulmonary disease (COPD), and occupational exposures that confer ahigh-risk of developing lung cancer. Clinical characteristics reportedat baseline such as sex, age, smoking status (ever or never) reported atbaseline visit, pack-years, prior history of lung cancer, COPD status,and occupational exposures were not significantly different between thetwo cohorts (Table 1). After sample filtering based on several qualitymetrics, the DC had 190 biopsies and 89 brushes while the VC had 105biopsies and 48 brushes. Ninety-four percent of subjects had at leastone lung anatomic location sampled 2 or more times via endobronchialbiopsy. The DC and VC contained 37.9% and 35.2% biopsies with ahistological grade of dysplasia or higher and 23.1% and 19.0% hadprogressive/persistent dysplasia, respectively (Table 2). A previouslydescribed smoking-associated signature (8) was used to predict thesmoking status of each sample, as smoking status was only available atbaseline, and found that the DC had a higher percentage of biopsiespredicted to be current smokers (62.6%) compared with the VC (36.2%).There is no significant difference in smoking status among the bronchialbrushings between the two cohorts since only 1 brush is collected pertime point. The predicted smoking status was consistent across allprocedures for 63% and 70% of the DC and VC subjects, respectively. Interms of RNA sequencing quality, the DC had significantly greater totalreads, percent uniquely mapping reads, and median transcript integritynumber scores among the biopsies than the VC, but these differencesbetween cohorts were not reflected in the brushes (FIG. 5 ).

LUSC PMLs within the Discovery Cohort Divide into Distinct MolecularSubtypes

In order to identify gene expression differences associated with LUSCPML histological severity using the endobronchial biopsies, adiscovery-based approach was used to identify de novo molecular subtypesbased on distinct patterns of gene co-expression (gene modules). Theapproach was chosen given that there is histological heterogeneitywithin biopsies and that pathological analyses were conducted usingbiopsies adjacent to biopsies profiled via mRNA-Seq. First, it wassought to select a set of gene modules that are present across differentLUSC datasets. Using weighted gene co-expression network analysis (9)(WGCNA), gene modules were derived in the DC biopsies (n=190 samples,n=16653 genes, n=15 gene modules), the DC brushes (n=89 samples, n=16058genes, n=47 gene modules), TCGA squamous cell carcinoma (LUSC) tumors(10) (n=471 samples, n=17887 genes, n=55 gene modules), andtracheobronchial samples from mice treated withn-nitrosotris-(2-choroethyl)urea (NTCU) (n=25 samples, n=14897 genes,n=40 gene modules). DC biopsy gene modules that were highly correlated(absolute Pearson correlation coefficient r>0.85) to at least one othernon-DC biopsy module within each of the 4 datasets were selected. Genesin the selected modules were filtered by requiring that each gene wasalso present in at least one of the correlated non-DC biopsy modules,resulting in a set of 9 gene modules that consisted of 3,936 genes intotal (FIG. 6 ). These gene modules identified 4 molecular subtypeswithin the DC biopsies via consensus clustering: Proliferative (darkblue, n=52 samples, 27.4%), Inflammatory (dark green, n=37 samples,19.5%), Secretory (light blue, n=61 samples, 32.1%), and Normal-like(light green, n=40 samples, 21.1%) (FIG. 1A, Table 3).

In order to characterize each molecular subtype, the first focus was onidentifying biological pathways over-represented in the genes comprisingeach gene module, as the pattern of gene module expression defines eachPML subtype. Each gene module was found to be associated with distinctepithelial and immune biological processes (FIG. 1A, FIG. 6 , and Table5). The Proliferative subtype is specifically characterized by increasedexpression of genes involved in energy metabolism and cell cyclepathways (Modules 4 and 5). The Secretory and Normal-like subtypes bothhave increased expression of genes in cilium-associated pathways (Module6), however, the Normal-like subtype specifically has decreasedexpression of genes involved in inflammation, regulation of lymphocytesand leukocytes, and antigen processing and presentation pathways(Modules 8 and 9). The Secretory subtype exhibits decreased expressionof genes involved in protein translation (Module 7), while RNAprocessing genes (Module 2) are expressed more highly in theInflammatory subtype.

The molecular subtypes were further characterized by their associationswith clinical phenotypes and established LUSC tumor molecular subtypes(11, 12). Sample smoking status, the subject from whom the sample wasderived, and sample histology demonstrated significant associations withsubtype (p<0.01, FIG. 1B, Table 6, FIG. 8 ). The Proliferative andSecretory subtypes are enriched for current smokers and this associationdrives the subject enrichment as 79% of subjects maintain their smokingstatus throughout the study. Additionally, the Proliferative subtype isenriched for biopsies with dysplasia histology (FIG. 1B). TheProliferative subtype has high expression of genes involved in cellcycle processes including the proliferation marker MKI67, which issignificantly up-regulated among samples in this subtype compared withsamples in other subtypes (FDR=1.0e-30, linear model, based ondifferential expression analysis between samples in the Proliferativeversus the non-Proliferative subtypes across all genes). The generemained significantly up-regulated in the Proliferative subtype withinsamples with normal/hyperplasia histology (FDR=3.4e-10, linear model)and samples with dysplasia histology (FDR=3.1e-8, linear model), andthese observations are supported by an increase in protein expression inrepresentative samples (p=0.02) (FIG. 1C-1E and FIG. 9 ). TheProliferative subtype samples also had high concordance with theLUSC-Classical subtype (FIG. 1B). In the TCGA LUSC tumors, theLUSC-Classical subtype was associated with alterations andoverexpression of KEAP1 and NFE2L2 as well as amplification of 3q26 withoverexpression of SOX2, TP63 and PIK3CA (11). Similarly, ourProliferative PMLs have increased expression of KEAP1, NFE2L2, TP63, andPIK3CA (FDR=1.4e-6, 4.5e-12, 1.4e-9, and 0.03, respectively, linearmodel) (FIG. 10A). Furthermore, the LUSC-Classical subtype was found tobe associated with increased expression of genes involved in energymetabolism, and our Proliferative subtype is in part defined by highexpression of Module 4, which is enriched for genes associated withoxidative phosphorylation and the electron transport chain. In contrast,the Inflammatory and Secretory PML subtypes demonstrate enrichment forthe LUSC-Secretory subtype. The LUSC-Secretory subtype was associatedwith processes related to the immune response, and the Inflammatory andSecretory PMLs have the highest expression of Module 8 that is enrichedfor genes in these same pathways.

Finally, the extent to which the PML molecular subtypes were driven bydifferences in epithelial and immune cell type composition by assessingexpression of a number of canonical cell type markers was examined. TheInflammatory and Secretory subtypes have higher levels of expression ofthe white blood cell marker PTPRC (CD45) consistent with enrichment ofthe LUSC-Secretory subtype (FIG. 10B, FDR=0.12 and 0.01, respectively,linear model). Consistent with the behavior and pathways enriched inModule 6, the ciliated cell marker TUB1A1 expression is decreased in theInflammatory and Proliferative subtypes (FDR=1.1e-4 and 3.5e-19,respectively, linear model), and this is also shown by a decrease inacetylated a-tubulin staining in representative histological samples(FIG. 1E, FIG. 9 ). The Proliferative subtype has the highest expression(FDR=2.4e-15.1 linear model) of basal cell marker (KRT5) indicatingenrichment of lesions with high-grade histology that tightly correlateswith protein expression in representative histology samples (p=0.01)(FIG. 1E, FIG. 9 , FIG. 10B, Table 7). Additionally, gene expression ofMUC5AC, a marker of goblet epithelial cells, is increased in subtypesenriched for current smokers (Proliferative and Secretory) but is themost significantly increased in the Secretory subtype (FDR=3.4e-5,linear model). In contrast, gene expression of SCGB1A1, a marker of clubcells, is the lowest in the Proliferative subtype (FDR=6.1e-5, linearmodel). The Normal-like subtype is supported by expression of allepithelial cell types and has the lowest expression of CD45 (FDR=7.6e-4,linear model). The expression levels of these marker genes agree withcell type deconvolution methods to examine epithelial and immune cellcontent (FIG. 10C-10D). The summation of these characterizationshighlights epithelial and immune cell associated pathways that aremodulated by smoking and PML histology and identifies the Proliferativesubtype as a subset of high-grade PMLs that express proliferative andcell cycle-related pathways.

Phenotypic Associations with the Molecular Subtypes are Confirmed in theValidation Cohort

Next, it was desired to determine if the heterogeneity captured in theDC biopsy-derived molecular subtypes was reproducible in the VC. A22-gene nearest centroid molecular subtype predictor was developed byselecting genes representative of each of the 9 gene modules. Thepredictor has 84.7% accuracy across DC biopsies (training set, FIG. 2Aand FIG. 11 ) with the following misclassification rates per subtype5/52 (9.6%) in Proliferative, 7/37 (18.9%) in Inflammatory, 9/61 (14.8%)in Secretory, and 8/40 (20%) in Normal-like. The 22-gene classifier wasused to predict the molecular subtype of the 105 VC biopsies (FIG. 2B).The VC subtype predictions were evaluated by examining the concordanceof metagene scores for each of the 9 modules (using the full set ofgenes for each module) between the predicted VC subtypes compared withthe DC subtypes. The average behavior of Principal Component 1 (PC1)across the subtypes was highly similar (FIG. 12 ) with few exceptions(namely, Module 3 that had the fewest genes). Additionally, the VCsubtype predictions from the 22-gene classifier were compared tosubtypes derived in the VC biopsies using the same methodology used toderive the DC subtypes and found significant concordance (p=1.0e-7, withthe Proliferative subtype having the greatest concordance betweenpredictions, FIG. 11 ).

The statistical associations between the VC subtypes (via the 22-geneclassifier) and clinical and molecular phenotypes across the VC biopsiesare analogous to those observed across the DC biopsies (FIG. 2C, Table6, FIG. 8 and FIG. 10A-10H). Briefly, the Proliferative subtype isenriched for current smokers, biopsies with dysplasia histology, and theLUSC-Classical tumor subtype (FIG. 2C, Table 6). Epithelial and whiteblood cell marker gene expression across the VC biopsies reveals higherlevels of the white blood cell marker PTPRC (CD45 expression) in theInflammatory subtype (FDR=0.002) consistent with enrichment of theLUSC-Secretory subtype (FIG. 10F).

The Inflammatory and Proliferative subtypes have reduced ciliated cellmarker expression (FOXJ1) consistent with Module 6 (FOXJ1 FDR=0.0005 andFDR=2.62e-6 and Module 6 FDR=5.73e-6 and FDR=4.34e-10, respectively).The Proliferative subtype has the highest expression of basal cellmarker KRT5 (FDR=1.67e-7), proliferation marker MK167 (FDR=3.03e-10),and cell cycle associated Module 5 (FDR=1.23e-18) indicating enrichmentof lesions expressing characteristics associated with high-gradehistology. Gene expression of SCGB1A1, a marker of club cells, is thelowest in the Proliferative subtype (FDR=1.8e-4). Gene expression ofMUC5AC, a marker of goblet epithelial cells, was increased in currentsmokers and most significantly in the Secretory subtype in the DCbiopsies; however, in the VC biopsies this trend is not preserved ascurrent smokers are not enriched in the Secretory subtype. Theexpression levels of these marker genes agree with other deconvolutionmethods to examine epithelial and immune cell content (FIG. 10E-10H).

Normal Appearing Airway Field Brushes Reflect Biopsy Molecular Subtype

Previously, it was shown that bronchial brushes from normal appearingareas of the mainstem bronchus could predict the presence of PMLs (13);however, that study lacked biopsies and brushes from the same subjects.Above, in both the DC and the VC biopsies, the Proliferative subtype,represents a distinct subtype of PMLs enriched for dysplastic histologyexpressing metabolic and proliferative pathways. Biopsies classified asthe Proliferative subtype may represent a group of PMLs that need closemonitoring and intervention. As a result, it was sought to explorewhether or not it was possible to predict the presence of Proliferativesubtype biopsies using the brushes. The Proliferative subtype is definedby the behavior of Modules 4, 5, 6, and 7 (Table 3), and therefore, thesubset of 8 genes (from the 22-gene predictor) that correspond to theseModules was used to predict the presence of the Proliferative subtypeacross the DC and VC biopsies and brushes. A prediction of theProliferative subtype in a brush is specific (91% and 92% in the DC andVC biopsies, respectively), but not sensitive (39% and 32% DC and VCbiopsies, respectively) at indicating the presence of at least oneProliferative PML detected at the same time point (FIG. 3A). In order tounderstand the classifier's performance in predicting the Proliferativesubtype in brushes, Gene Set Variation Analysis (GSVA)(14) scores wereexamined for Modules 4, 5, 6, and 7 that define the Proliferativesubtype in the DC and VC brushes (FIG. 3B). In the DC and VC brushes,the GSVA scores were significantly different (FDR<0.05) in theProliferative subtype versus all other samples only for Modules 5 and 6,and thus these likely contribute the most heavily to Proliferativesubtype classification in the brushes. Module 5 contains genesassociated with cell cycle and proliferation while Module 6 containsgenes associated with cilium assembly and organization. Down-regulationof Modules 5 and 6 in the brushes specifically predicts the presence ofa Proliferative subtype PML; however, the absence of these signals inthe airway field of injury does not preclude the development of aProliferative subtype PML.

Immune-associated genes separate proliferative subtypeprogressive/persistent and regressive PMLs. Previous studies ofbronchial PMLs suggest that high-grade lesions (which occur morefrequently in current smokers) are more likely to progress to invasivecarcinoma (6). Therefore, it was sought to identify molecularalterations associated with subsequent PML progression/persistence(n=15) versus regression (n=15) among the Proliferative subtype DCbiopsies, as these may be clinically relevant to identifying appropriateinterception strategies. Using GSVA scores calculated across all the DCbiopsies for each of the 9 modules, it was calculated which scores werestatistically different between progressive/persistent versus regressivedisease in the samples belonging to the Proliferative subtype (FIG. 7 ).It was found that the DC biopsy GSVA Module scores for Module 9 weresignificantly higher among regressive Proliferative PMLs (p=0.002,linear model FIG. 4A) compared with progressive/persistent ProliferativePMLs. The association between low Module 9 score andprogression/persistence is replicated in the VC biopsies (n=7progressive/persistent and n=13 regressive biopsies; p=0.03, linearmodel FIG. 4B). The ability of the Module 9 GSVA scores to discriminatebetween regressive versus progressing/persistent biopsies as measured bythe area under the receiver operating characteristic (ROC) was 0.809 and0.802 in the DC and VC biopsies, respectively.

The genes in Module 9 include a number of genes that encode for proteinsinvolved in interferon signaling as well as antigen processing andpresentation (SP100, CIITA, CXCL10, SOCS1, GBP1, GBP4, B2M, TAP1, TAPBP,TRIM 14, TRIM21, TRIM122, STAT1, PML, OAS2, OAS3, MX1, ADAR, ISG15,IFI35, IFIT3, IFI27, PSMB8, PSMB9, BST2, IRF1, IRF9, CD74, PSME1, PSME2,HLA-DQA1/DPA1/DPB1/DRA/DQB2/DRB1/DQB1/DMA/DMB/D0A, HLA-A/B/C/E/F) andinclude the inhibitory receptor LAGS. As a result, it was wanted toevaluate whether or not the presence or absence of innate or adaptiveimmune cells were associated with Module 9 expression within theProliferative subtype. In an effort to deconvolute the potentialpresence of immune cell types, GSVA scores were generated usingpreviously described immune cell signatures (15) and scores for 64different cell types using the xCell algorithm (16), separately for boththe DC and VC biopsies. Significant (FDR<0.05) associations wereidentified between the cell type scores and Module 9 that were in commonbetween the DC and VC biopsies (FIG. 13 ) and 8 cell types identified(via xCell) including dendritic cells, activated dendritic cells,plasmacytoid dendritic cells, macrophages, M1 macrophages as well asCD8+ effector memory T cells, CD8+ central memory T cells, and Tregulatory cells (FIG. 4C). Taken together, the progressive/persistentbiopsies in the Proliferative subtype have down-regulated expression ofModule 9 compared with regressive biopsies that correlates with reducedsignals from both innate and adaptive immune cell populations.

Immunofluorescence Reveals Progression-Associated Modulation ofMacrophages and T Cells in Proliferative PMLs

In order to confirm the relationship between the immune cell typesassociated with Module 9 and histologic progression/persistence of PMLsin the Proliferative subtype, immunofluorescent staining ofmacrophages/monocytes (n=52 regions enumerated from n=16 subjects), CD4(n=50 regions enumerated from n=17 subjects), and CD8 T cells (n=47regions enumerated from n=16 subjects) was performed (Table 7). Theresults were analyzed across all subjects assayed within theProliferative subtype and across the subset of subjects where the lesionoutcome (progression/persistence versus regression) was concordant withthe Module 9 GSVA score (denoted as concordant set). Staining of CD68, apan macrophage (and tumor associated macrophage) marker, suggestive ofM1 type macrophages, was increased in progressive/persistent lesions(p<<0.001 in the concordant set). In contrast, staining of CD163 incombination with CD68, thought to be suggestive of M2 type macrophages,were decreased among the progressive/persistent lesions in theProliferative subtype (p<<0.001 using all subjects and p=0.0007 in theconcordant set, respectively, linear model) (FIG. 4D-4E). Additionally,CD4 T cells were increased (p<<0.001 in the concordant set, linearmodel) and CD8 T cells were decreased (p<<0.001 in the concordant set)in PMLs that progress/persist. Interestingly, amongprogressive/persistent lesions, the CD8 T cells had a distinctlocalization pattern (p=0.07 in the concordant set, linear model), whereCD8 T cells both lined and were embedded within the epithelium in areaswhere dysplasia is present (FIG. 4D). The immunofluorescence results didnot reach significance, with the exception of CD163, when just thelesion outcome was used without regard to the Module 9 score.

Discussion

Lung squamous cell carcinoma (LUSC) is the second most common form oflung cancer and arises in the epithelial layer of the bronchial airways.It is often preceded by the development of lung squamous premalignantlesions (PMLs). The presence of dysplastic persistent and or progressivePMLs is a marker of increased risk for LUSC (6). Currently, however,effective tools to identify PMLs at highest risk of progression toinvasive carcinoma are lacking (7). The development of markerspredictive of disease progression will be important in identifyingpatients at highest risk for LUSC development and in identifyingbiological pathways exploitable for LUSC chemoprevention. Towards thisgoal, described herein is profiling via RNA-Seq bronchial brushes andendobronchial biopsies obtained from subjects undergoing longitudinallung cancer screening by chest computed tomography (CT) andautofluorescence bronchoscopy. Four transcriptionally distinct groups ofbiopsies are identified, one of these labelled Proliferative and foundto be associated with high-grade dysplasia. Patients with ProliferativePMLs can also be identified via gene expression measured from cells inthe non-involved large airway epithelium. It was further found thatpersistent/progressive Proliferative PMLs are characterized by decreasedexpression of genes involved in interferon signaling and antigenprocessing/presentation pathways. Consistent with these gene expressionfindings it was found that progressive/persistent Proliferative PMLs aredepleted for CD68+/CD163+ macrophages and CD8 T cells byimmunofluorescence. Collectively, these data indicate both the potentialto identify a subset of patients with progressive/persistent LUSC PMLs,who are at risk for developing invasive lung cancer, on the basis ofairway gene expression; as well as the potential to decrease the riskfor progression in these patients by augmenting the immune responseassociated with regression.

Previous studies indicate a range of genomic alterations associated withbronchial dysplasia. Increased expression of EGFR and Ki67 staining ofepithelial cells is associated with increasing histologic severity andsubsequent histologic progression (6, 17). Altered protein levels ofTP53, CCND1, CCNE1, BAX, and BCL2 have been associated with CIS or lungcancer occurrence independent of histological grade (18). Telomereshortening and maintenance (19) and loss of heterozygosity in regionsfrequently detected in lung cancer (3p, 5q, 9p, 13q, 17p) have beenobserved in early hyperplasia/metaplasia lesions (20-22) and found toincrease in frequency and size in higher-grade dysplasia. Genomic gainsin loci containing SOX2, TP63, EGFR, MYC, CEPS, and CEPS are alsoassociated with progression of high-grade dysplasia (23). Despite thenumerous genomic alterations associated with PML histological grade andprogression, a comprehensive PML molecular classification system tocomplement the pathologic classification of PML is lacking. Use of anunsupervised class discovery approach that led to the identification offour distinct molecular PML subtypes (Proliferative, Inflammatory,Secretory, and Normal-like).

The transcriptional patterns differentiating the PML subtypes are robustand a 22-gene panel identified in the Discovery Cohort can be used todistinguish between the different molecular subtypes in an independentValidation Cohort. Interestingly, while prior lung cancer history mayinfluence airway gene expression and about two-thirds of the subjectshave a prior history of lung cancer, we do not detect a significantassociation between lung cancer history and molecular subtype, and thereis a similar diversity of molecular subtypes between biopsies collectedfrom subjects with and without a lung cancer history. The Proliferativesubtype is enriched with dysplastic PMLs from current smokers and ischaracterized by up-regulation of metabolic (OXPHOS/ETC/TCA) and cellcycle pathways and down-regulation of cilia-associated pathways.Previous work indicates increases in metabolic pathways in the airwaysof subjects with dysplastic lesions (13), in PMLs adjacent to LUSC tumor(24), and in smokers at high-risk for lung cancer (25) as well asincreases in proliferation (via Ki67 levels, as mentioned above) thathave been utilized as an endpoint in lung cancer chemoprevention (26,27). Identification of patients with Proliferative lesions are useful toenrich lung cancer chemoprevention trials with high-risk subjects or toidentify patients who would benefit from more frequent lung cancerscreening. The Inflammatory subtype is predominated by PMLs from formersmokers, but interestingly is not significantly enriched for dysplasia,despite similarly decreased expression of cilia-associated pathways,suggesting an abnormal epithelium. The Inflammatory subtype also showsincreased expression of a gene module enriched for genes involved ininflammation and regulation of lymphocytes and leukocytes (Module 8).This gene module is also elevated in Secretory lesions predominated bylesions from current smokers and exhibiting increased expression ofgoblet cell markers. Interestingly, IL1B is part of thisinflammation-related gene module, which is of great interest as theinhibition of IL1B has recently been shown to reduce lung cancerincidence (28).

Our prior work has extensively studied gene expression alterations innormal-appearing airway epithelium by profiling cells obtained viabrushing the mainstem bronchus during bronchoscopy (8, 29,35). As partof this work, gene expression alterations were described that reflectthe presence of bronchial dysplasia (31). In the current study, for thefirst time both bronchial brushes and endobronchial biopsies werecollected during the same procedure allowing identification of geneexpression differences in bronchial brushings from normal appearingairway which indicate the presence of Proliferative subtype PMLs. Inboth the Discovery and Validation cohorts, applying the predictor usedto identify Proliferative subtype PMLs (based on PML biopsy geneexpression) to the gene expression data from the normal-appearing airwaybrushings resulted in predictions of the Proliferative subtype that werevery specific (91%) but not sensitive (31-38%). Brushes classified asProliferative have increased expression of cell cycle pathways anddecreased expression of cilia-associated genes, suggesting that they aremore similar to squamous metaplasia than normal epithelium. Potentially,a subset of patients may harbor widespread airway damage that serves asa marker for the presence of this type of high-grade PML leading tomodest sensitivity, but high specificity. In other cases, the area ofdamage that gives rise to these Proliferative PMLs may be morelocalized, and therefore potentially more difficult to detect bybrushing contributing to decreased sensitivity. These findings indicatethat therapeutics to target changes throughout the entire airwayepithelium may be necessary in some subjects, whereas, moresite-specific ablation (e.g. photodynamic therapy) may be more effectivein certain cases. Another possibility and area of future research, isthat a Proliferative subtype brush is a predictor of incident LUSC.

The molecular profiling of PMLs and the identification of geneco-expression modules also provides an opportunity to identify themolecular determinants of subsequent PML progression. One of the ninegene co-expression modules used to define the molecular subtypes wassignificantly different between biopsies that progress or persistcompared to biopsies that regress within the Proliferative subtype inboth the DC and VC cohorts. The module contains genes whose expressionis decreased in the persistent/progressive biopsies that are involved ininterferon signaling and antigen processing and presentation. These geneexpression changes were correlated with a decreased abundance of innateand adaptive immune cells via computational prediction. Byimmunofluorescent staining of FFPE biopsy sections it was confirmed thatthe progressive/persistent Proliferative lesions with low Module 9 GSVAscores had fewer CD163+ macrophages and CD8+T cells and the CD8+T cellshad a distinct localization pattern. These lesions also containedgreater numbers of CD4+ T cells, and it will be important in future workto assess if these cells are T regulatory cells promoting an immunesuppressive environment.

The presence of tumor-associated macrophages with the polarizedphenotypes (M1 as pro-inflammatory or M2 as anti-inflammatory) has beenassociated with lung cancer prognosis. The presence of predominantly M2macrophages, marked by the expression of CD163, has been associated withworse survival. However, in the context of lung PMLs this relationshipis not well studied. The present finding that regressive ProliferativePMLs have more CD163+ cells and increased expression of genes involvedin IFNg signaling is consistent with what has been seen in the PMLs thatprecede oral squamous cell carcinoma where the presence of CD163+macrophages with active IFNg signaling is associated with betteroutcomes (36). Additionally, fewer CD8+ T cells and lower expression ofHLA class I genes and B2M were observed in progressive/persistentlesions within the Proliferative subtype. Disruptions in proper T cellmediated immunosurveillence have been described in several studiesshowing that impaired HLA class I antigen processing and presentationincluding down-regulation or loss of B2M (37, 38) and interferonsignaling (39) in lung tumors affects response and acquired resistanceto checkpoint inhibitors. Lung tumors lacking an HLA-I complex had lowercytotoxic CD8+ lymphocyte infiltration, and this was also associatedwith lower levels of PD-L1. Additionally, studies have also suggestednegative impacts on efficacy of check point inhibitors as well assurvival in patients with LC that have tumors with increased CD4+ Tcells expressing T regulatory markers (FOXP3, CD25) resulting inimmunosuppressive state suggested to hinder the recruitment and effectorfunctions of CD8+ T cells (40, 41). Future DNA sequencing data on thePMLs profiled here may indicate heterozygous or homozygous loss of B2Mor mutations in other genes in the interferon and antigen processing andpresentation pathways; however, even in the case of acquired resistance,mutations and copy number changes could not explain the down-regulationof these pathways across all subjects, suggesting that other epigeneticalterations or signaling pathways may play a role. In fact, epigenetictherapy, specifically DNA methyltransferase inhibitors (42), has beenshown to enhance response to immune checkpoint therapy and up-regulatemany of the genes down-regulated in progressive/persistent lesionswithin the Proliferative subtype including HLA class I genes (HLA-B andHLA-C), B2M, CD58, TAP1, immune-proteasome subunits PSMB9 and PSMB8, andthe transcription factor IRF9. Unraveling the mechanisms of innate andadaptive immune down-regulation in this subset of PMLs will be importantto identifying potential immunoprevention therapies.

The present data indicates that there are subtype-specifictranscriptomic alterations predictive of subsequent LUSC premalignantlesion progression that are the result of a lack of infiltrating immunecells in the lesion microenvironment. These data suggest that biomarkersfor determining PML subtype and assessing immune infiltration may haveutility for the detection of aggressive PMLs that require more intensiveclinical management and genes altered in these PMLs may serve as lungchemoprevention candidates. These biomarkers could either be measureddirectly in PML tissue, or as indicated by the present data, they can bemeasured in a surrogate tissue such as bronchial airway epithelium. Abenefit of biomarkers predicting aggressive PML behavior measured insurrogate tissue is the potential that these biomarkers can also predictthe behavior of PMLs not directly observed during bronchoscopy.

Materials and Methods

Subject Population and Sample Collection

Endobronchial biopsies and brushings were obtained from high-risksubjects undergoing lung cancer screening at approximately 1-yearintervals by white light and auto-fluorescence bronchoscopy and computedtomography at Roswell. The bronchoscopy included visualization of thevocal cords, trachea, main carina, and orifices of the sub-segmentalbronchi visible without causing trauma to the bronchial wall. Allabnormal and suspicious areas are biopsied twice and the lung anatomiclocation is recorded (FIG. 14 , Table 8). One biopsy was used forroutine pathological evaluation and the other for molecular profiling.Additionally, a brushing was obtained from a normal appearing area ofthe left or right mainstem bronchus for research. Morphological criteriaused to evaluate the biopsies are in accordance with World HealthOrganization (WHO) guidance (43). Eligibility for screening includeseither a previous history of aerodigestive cancer and no disease at thetime of enrollment or age greater than 50, a current or previous historyof smoking for a minimum exposure of 20 pack-years and at least oneadditional risk factor including moderate chronic obstructive pulmonarydisease (COPD) (defined as forced expiratory volume (FEV1)<70%),confirmed asbestos related lung disease or a strong family history oflung cancer (at least 1-2 first degree relatives). All researchspecimens were stored in RNA Allprotect (Qiagen) and stored at −80degrees C.

Subjects were selected that had biopsies collected in repeat locationsvia serial bronchoscopies; however, after RNA isolation, samples from 3subjects had a single biopsy and 1 subject had a single brushing. mRNAsequencing was performed on a discovery cohort (DC) of samplescomprising of endobronchial biopsies and brushes collected between 2010and 2012 (n=30 subjects, n=197 biopsies, and n=91 brushings). mRNAsequencing was subsequently performed on a validation cohort (VC) ofsamples comprising of endobronchial biopsies and brushes collectedbetween 2012 and 2015 (n=20 subjects, n=111 biopsies, and n=49brushings). Brush histology was defined by the worst biopsy histologyobserved at the same time point. Biopsy progression/regression wasdefined for each biopsy based on the histology of the biopsy and theworst histology recorded for the same lung anatomic location in thefuture. Histology changes between normal, hyperplasia, and metaplasiawere classified as “normal stable”, decreases in histological dysplasiagrade or changes from dysplastic histology tonormal/hyperplasia/metaplasia were classified as “regressive”, lack offuture histological data was classified as “unknown”, and everythingelse was classified as “progressive/persistent.” The InstitutionalReview Boards at Boston University Medical Center and Roswell approvedthe study and all subjects provided written informed consent.

RNA-Seq Library Preparation, Sequencing, and Data Processing

Total RNA was extracted from endobronchial biopsies and bronchialbrushings using miRNeasy™ Mini Kit or AllPrep™ DNA/RNA/miRNA UniversalKit (Qiagen). Sequencing libraries were prepared from total RNA samplesusing Illumina TruSeq™ RNA Kit v2 and multiplexed in groups of fourusing Illumina TruSeq™ Paired-End Cluster Kit. Each sample was sequencedon the Illumina HiSeq™ 2500 to generate paired-end 100-nucleotide reads.Demultiplexing and creation of FASTQ files were performed using IlluminaCASAVA™ 1.8.2 or BaseSpace. Samples were aligned using hg19 and 2-passSTAR (44) alignment. Gene and transcript level counts were calculatedusing RSEM (45) using Ensembl™ v74 annotation. Quality metrics werecalculated by STAR and RSeQC (46). Samples were excluded were sexannotation did not correlate with gene expression across CYorf15A(ENSG00000131002), DDX3Y (ENSG00000067048), KDM5D (ENSG00000012817),RPS4Y1 (ENSG00000129824), USP9Y (ENSG00000114374), and UTY(ENSG00000183878) (n=4 samples). Sample relatedness within a patient wasconfirmed using Peddy™ software (47).

Samples with a high-rate of heterozygosity (more than 3 standarddeviations above the median) or samples with low relatedness to samplesfrom the same patient (more than 3 standard deviations below the median)were removed from further analyses (n=11 samples, 2 brushes and 9biopsies). Samples were subsequently divided into the discovery andvalidation cohorts (as outlined above) and by tissue type (biopsy orbrush). Subsequent sample and gene filtering was conducted separately oneach set as follows: First, EdgeR™ (48) was used to compute normalizeddata (library sizes normalized using TMM, trimmed mean of M-values, andlog 2 counts per million computed) and genes were excluded that eitherhad an interquartile range equal to zero or a sum across samples equalor less than 1. Samples were excluded based on values greater than 2standard deviations from the mean for more than one of the followingcriteria: 1) mean Pearson correlation with all other samples calculatedacross all filtered genes 2) the 1^(st) or 2^(nd) principal componentscalculated using the filtered gene expression matrix 3) transcriptintegrity number (TIN, computed by RSeQC). After sample filtering, genefiltering was recomputed as described above on the final set ofhigh-quality samples. The data are available from NCBI's Gene ExpressionOmnibus using the accession GSE109743.

Derivation of Molecular Subtypes

The DC biopsies (n=190 samples, n=16653 genes) and brushes (n=89samples, n=16058 genes) were used to derive the molecular subtypes. Twoadditional RNA-Seq datasets were used during the derivation of themolecular subtypes: the TCGA squamous cell carcinoma (LUSC) tumors (10)(n=471 samples, n=17887 genes) and a dataset of tracheobronchial samplesfrom mice treated with n-nitrosotris-(2-choroethyl)urea (NTCU) (n=25samples, n=14897 genes). The mice develop lesions that arehistologically and molecularly comparable to human lesions and thatprogress to LUSC and the samples represent a range of histology (normal,mild dysplasia, moderate dysplasia, severe dysplasia, carcinoma in situ(CIS), and LUSC tumor). The mouse data are available from NCBI's GeneExpression Omnibus using the accession ID GSE111091. Sample and genefiltering from the TCGA LUSC tumors and the mouse tissue were processedas described elsewhere herein.

Weighted correlation network analysis (9) (WGCNA) was used with defaultparameters to derive Modules of gene co-expression across the 4 datasetsdescribed above. Residual gene expression values adjusting for RNAquality (median TIN) and batch (Illumina flow cell) were used as inputfor WGCNA for the biopsy and brush datasets. For the mouse dataset,residual gene expression values adjusting for RNA quality (median TIN),mouse strain, and sample type (laser capture microdissected versus wholetissue) were used as input for WGCNA. Log 2 counts per million (cpm)values were used as input for WGCNA for the LUSC tumor samples. Genesets were created for each co-expression Module for each dataset andthen combined to create a compendium of gene sets generated from each ofthe 4 datasets. For each gene set in the compendium, the first principalcomponent (PC1) was calculated across each z-score normalized dataset.For each dataset, a Pearson correlation matrix of PC1 values across allgene sets in the compendium was computed and thresholds were set asfollows: r>0.85 was set to 1 and r<=0.85 set to 0. The four matriceswere subsequently summed, and gene sets derived from biopsyco-expression Modules that were correlated to another non-biopsy derivedgene set across all datasets were retained (n=9 Modules retained). Thegenes defining the retained biopsy Modules were required to be presentin the biopsy Module and at least in one of the correlated gene sets.

The filtering process above yielded a reduced set of genes (n=3,936)that was used to define the molecular subtypes in the biopsy data. Theresidual gene expression values across the reduced set of genes for thediscovery biopsies was used as input for consensus clustering (49).Consensus clustering was performed setting k (number of groups) to 10,the number of iterations to 1000, the subsampling to 80%, the clusteringalgorithm to partitioning around mediods, and the distance metric toPearson correlation. The optimal value for k was 4 based on the relativechange in area under the cumulative distribution function calculatedbased on the consensus matrix for each k.

Molecular Subtype Predictor

The DC biopsies across the filtered genes were used to derive amolecular subtype predictor. First, Pearson correlation metrics weredetermined between each gene and the Module eigengenes (PC1 for each ofthe 9 Modules). Genes were retained as part of a Module if thecorrelation value was the highest for the Module in which it wasassigned. The average Pearson correlation of the retained genes to theModule eigengene was computed, and the number of genes chosen from eachModule for the predictor was inversely proportional to this metric.Second, the genes most highly correlated to the Module eigengene werechosen to represent the Module in the predictor. The 22 genes resultingfrom this analysis across the DC biopsy data were used to train anearest centroid predictor using the pamr package with a threshold ofzero and predict the molecular subtype across the VC biopsies. Prior topredicting the molecular subtype of these test sets, the training andtest sets were combat (50) adjusted and z-score normalized acrosscombined training and test data. Using the methods described above wederived molecular subtypes using consensus clustering across the VCbiopsies and compared these to the predicted subtypes.

Identification of Biological Processes Associated with Gene Modules andMolecular Subtypes

Biological processes and pathways enriched in each of the nine Modulesused to discover the molecular subtypes in the DC were identified usingEnrichR (51). Each Module was separated into genes positively ornegatively correlated with the Module eigengene, the Ensembl IDs wereconverted to Gene Symbols using biomaRt, and the following databaseswere queried: GO Biological Process 2015, KEGG 2016, WikiPathways 2016,TargetScan microRNA, Transcription Factor PPIs, TRANSFAC and JASPARPWMs, OMIM Disease, Reactome 2016, and Biocarta 2016. Processes/pathwayswith an FDR<0.05 were considered to be significantly enriched. Thecontribution of each gene Module to the DC biopsy molecular subtypes wasevaluated by testing if GSVA (14) scores for each Module weresignificantly (FDR<0.05) associated with the molecular subtypes using alinear mixed effect model with patient as a random effect via limma.

Identification of Clinical and Biological Phenotype Associations withMolecular Subtype

The molecular subtypes in the DC biopsies were annotated according tothe behavior of each gene Module by calculating whether or not GSVA (14)scores for each Module were significantly up- or down-regulated(FDR<0.05) in a particular molecular subtype versus all other samplesusing a linear mixed effects model with patient as a random effect vialimma. Additionally, the biological pathways and transcription factorsassociated with each subtype were identified using GSEA (52) and mSigDB(53) gene sets using genes ranked by the t-statistic for theirassociation with each subtype. The ranked lists were created using thelimma (54) and edgeR (48) packages to identify differentially expressedgenes associated with subtype membership.

Each linear model used voom-transformed (55) data and includedmembership in the subtype of interest, batch, and RNA quality (TIN) ascovariates and patient as a random effect. Pathways enriched in theranked lists (FDR<0.05) were used to annotate the molecular subtypes.FDR values for individual genes were derived from this analysis oranalogous models using only samples of normal/hyperplasia histology ordysplasia histology.

For the DC and VC biopsies, residual gene expression values were used topredict smoking status, LUSC tumor subtype, and the relative abundanceof epithelial and immune cells for each sample. Smoking status (currentversus former/never) was predicted for each sample as describedpreviously (13). Smoking status was determined at each time point foreach subject by calculating the mean of the prediction scores (>0 forcurrent prediction and <0 for former/never prediction) across allbiopsies and brushes sampled. The LUSC tumor subtype was determined asdescribed previously (11) across the genes predictive of the LUSCmolecular subtype (12). The ESTIMATE algorithm (56) was used to inferrelative epithelial, stromal, and immune cell content. Immune cell typespecific signatures from Bindea et al. (15) and epithelial cell typespecific signatures from Dvorak et al. (50) were used to generateGSVA(14) scores across samples for each signature. Additionally,residual gene expression values calculated using log RPKM values wereinputted into the xCell (16) to infer relative abundances of 64different cell types. The above categorical phenotypes along withadditional clinical variables such as biopsy histology, subject,previous lung cancer history, sex, and biopsy progression/regressionstatus were associated with molecular subtype using Fisher's Exact Test.Continuous variables were associated with molecular subtype using alinear model via limma.

In order to characterize the molecular alterations associated withlesion outcome, a linear mixed effects model was used to assess moduleGSVA score differences between progressive/persistent versus regressivelesions within each molecular subtype with patient as a random effectvia limma. We estimated differences in the immune cell content(separately for xCell and Bindea et al.) between progressive/persistentversus regressive lesions in the Proliferative subtype via a linearmixed effects model correcting for epithelial cell content (‘Epithelial’in xCell and ‘Normal mucosa’ in Bindea et al.) and patient as a randomeffect. We focused on cell types that were significantly different(FDR<0.05) between progressive/persistent versus regressive lesions inthe Proliferative subtype in both the discovery and validation cohorts.

Relationship Between the Biopsies and Brushes

It was desired to quantify the predictive performance of the brush withregards to the presence of a biopsy of the Proliferative subtype. Asubset of the 22-gene molecular subtype predictor was used to predictthe presence or absence of the Proliferative subtype across the DC andVC brushes and biopsies. Specifically, 8 genes (out of the 22) were usedthat corresponded to Modules 4 through 7 (significantly up- ordown-regulated in the Proliferative subtype) to classify samples asProliferative or not using the same methodology described above for themolecular subtype predictor. Sensitivity and specificity performancemetrics were calculated based on the ability of a Proliferative subtypeprediction in the DC or VC brushes to indicate the presence of at leastone biopsy of the Proliferative subtype. In order to further understandthe Proliferative subtype predictions in the brushes, the behavior ofthe modules that define the Proliferative subtype in the DC biopsies(based on methods above) was analyzed across the DC and VC brushes.

Immunofluorescent Staining and Quantitation

Standard formalin fixation and embedding techniques were employed atRoswell where 5-micron sections were cut from the FFPE samples used forthe routine pathological evaluation at Roswell (Table 7). Prior tostaining, samples were de-waxed with xylene and rehydrate through agraded series of ethanol solutions. AR or citrate buffer was used forantigen retrieval, tissue was incubated with primary antibodiesovernight at 4° C. and probed with secondary antibodies with fluorescentconjugates (Invitrogen Alexa Fluor 488, 594, 647) for 1 hour at roomtemperature. Immunostaining was performed using the primary antibodieslisted in Table 9. Imaging was performed using an Aperio Slide Scannerfor scoring and a Carl Zeiss Axio (20× and 40× objectives) and a CarlZeiss LSM 710 NLO confocal microscope for capturing additional images.Digital slides were analyzed with the Definiens Tissue Studio (DefiniensInc.) for the enumeration of immunofluorescence staining. Theenumeration of the immunofluorescence scored each stain including DAPIpositive cells. The enumeration was conducted on different regions(independent areas of tissue) present on a slide (1-5 regions/biopsy)for each biopsy. For each region, the percentage of positively stainingcells for a given protein was calculated by dividing the number ofpositively stained cells by the total number of DAPI positive cells. Abinomial mixed effects model via the 1me4 R package was used to assessdifferences in the percentages of cells staining positive for a givenprotein in each region between progressive/persistent versus regressivebiopsies using the total cells stained in each region as weights andadjusting for the slide number as a random effect. The models were usedacross samples from the Proliferative subtype and across samples fromthe Proliferative subtype where the biopsy outcome(progressive/persistent versus regressive) agreed with the Module 9 GSVAscore (scores less than 0 are associated with progression/persistenceand scores greater than 0 are associated with regression). Each regionwas also qualitatively scored as either positive or negative for havinga distinct CD8 T cell localization pattern where cells lined and wereembedded within the epithelium.

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TABLE 1 Demographic and Clinical Annotation on Subjects in both theDiscovery and Validation cohorts. Statistical tests between theDiscovery and Validation cohorts were performed using Fisher's ExactTest for categorical variables and Student's T-Test for continuousvariable. Percentages are reported for categorical variables and meanand standard deviations are reported for continuous variables. DiscoveryValidation Cohort Cohort (n = 30 (n = 20 p- Variable Subjects) Subjects)value Average # Biopsies/Subject 6.6 (5.7) 5.25 (2.9) 0.3 Average #Bronchoscopies/Subject 2.8 (1.5) 2.4 (0.8) 0.27 Average Time BetweenBronchoscopies (Days) 368.2 (201.4) 360.1 (212.5) 0.87 Male 15/30 (50)12/20 (60) 0.57 White 27/30 (90) 17/20 (85) 0.67 Age (at BaselineClinical Visit) 58.8 (7.6) 58.7 (8.3) 0.97 Ever smoker (at Baseline29/30 (96.7) 19/20 (95) 1 Clinical Visit) Prior History of Lung Cancer21/30 (70) 12/20 (60) 0.55 COPD (FEV1/FVC <=0.7, at Baseline ClinicalVisit) 17/27 (63.0) 8/18 (44.4) 0.24 GOLD 1 (FEV1% >80) 2/27 (7.4) 2/18(11.1) 1 GOLD 2 (FEV1% <80 and >50) 12/27 (44.4) 5/18 (27.8) 0.35 GOLD 3(FEV1% <50 and >30) 3/27 (11.1) 1/18 (5.6) 0.64 Occupational Asbestos13/30 (43.3) 9/20 (45) 1 Occupational High-Risk Job 14/30 (46.7) 12/20(60) 0.4 Discovery Validation Cohort Cohort P- Variable (n = 30) (n =20) value Average # Biopsies/Subject 6.6 (5.7) 5.25 (2.9) 0.3 Average #Bronchoscopies/Subject 3.1 (1.6) 2.5 (0.7) 0.08 Average Time Between348.6 (197.5) 366.8 0.69 Bronchoscopies (Days) (208.3) Male 15/30 (50)12/20 (60) 0.81 White 27/30 (90) 17/20 (85) 1 Age (at Baseline ClinicalVisit) 58.8 (7.6) 58.7 (8.3) 0.97 Ever smoker (at Baseline 29/30 (96.7)19/20 (95) 1 Clinical Visit) Pack-years 49.8 (22.1) 41.3 (20.7) 0.17Prior History of Lung Cancer 21/30 (70) 12/20 (60) 0.82 LUSC 5/30 (16.7)5/20 (25) 0.73 Other 16/30 (53.3) 7/20 (35) 0.6 COPD (FEV1/FVC <=0.7, at17/27 (63.0) 8/18 (44.4) 0.61 OLD 1 (FEV1% >80) 2/27 (7.4) 2/18 (11.1) 1Baseline Clinical Visit) GOLD 2 (FEV1% <80 and >50) 12/27 (44.4) 5/18(27.8) 0.56 GOLD 3 (FEV1% < 50 and >30) 3/27 (11.1) 1/18 (5.6) 1Occupational Asbestos 13/30 (43.3) 9/20 (45) 1 Occupational High-RiskJob 14/30 (46.7) 12/20 (60) 0.62

TABLE 2 Clinical Annotation on Samples in both the Discovery andValidation cohorts. Statistical tests between the Discovery andValidation cohorts within either the biopsies or brushes were performedusing Fisher's Exact Test and percentages are reported. VariableDiscovery Cohort Validation Cohort P-value Sample Type Biopsies BrushesBiopsies Brushes Biopsies Brushes Histology 0.05 0.42 Normal 38/190 (20)6/89 (6.7) 23/105 (21.9) 0/48 (0) Hyperplasia 30/190 (15.8) 11/89 (12.4)31/105 (29.5) 9/48 (18.8) Metaplasia 46/190 (24.2) 15/89 (16.9) 14/105(13.3) 9/48 (18.8) Mild Dysplasia 21/190 (11.1) 9/89 (10.1) 13/105(12.4) 6/48 (12.5) Moderate Dysplasia 38/190 120) 30/89 (33.7) 20/105(19.0) 18/48 (37.5) Severe Dysplasia 12/190 (6.3) 17/89 (19.1) 4/105(3.8) 6/48 (12.5) CIS 1/130 (0.5) 0/89 (0) 0/105 (0) 0/48 (0) Tumor0/190 (0) 1/89 (1.1) 0/105 (0) 0/48 (0) Unknown Histology 4/190 (2.1)0/85 (0) 0/105 (0) 0/48 (0) Current smoker 119/190 (62.6) 44/89 (49.4)38/105 (36.2) 20/48 (41.7) 1.80E−05 0.47 (Genomic prediction)Progression Status 0.39 Normal/Stable 47/190 (24.7) 35/105 (33.3)Progressive/Persistent 44/190 (23.2) 20/105 (19.0) Regressive 30/190(15.8) 18/105 (17.1) Unknown 69/190 (36.3) 32/105 (30.5) Histology 0.050.42 Normal 38/190 (20) 6/89 (6.7) 23/105 (21.9) 0/48 (0) Hyperplasia130/89 (33.7) 11/89 (12.4) 31/105 (29.5) 9/48 (18.8) Metaplasia 46/190(24.2) 15/89 (16.9) 14/105 (13.3) 9/48 (18.8) Mild Dysplasia 21/190(11.1) 9/89 (10.1) 13/105 (12.4) 6/48 (12.5) Moderate Dysplasia 38/190(20) 30/89 (33.7) 20/105 (19.0) 18/48 (37.5) Severe Dysplasia 12/190(6.3) 17/89 (19.1) 4/105 (3.8) 6/48(12.5) CIS 1/190 (0.5) 0/89 (0) 0/105(0) 0/48 (0) Tumor 0/190 (0) 1/89 (1.1) 0/105 (0) 0/48 (0) UnknownHistology 4/190 (2.1) 0/89 (0) 0/105 (0) 0/48 (0)

 ent smoker (Genomic prediction) 122/190 (64.3) 50/89 (56.2) 53/105(50.5) 27/48 (56.3) 0.03 1 Progression Status 0.39 Normal/Stable 47/190(24.7) 35/105 (33.3) Progressive/Persistent 44/190 (23.2) 20/105 (19.0)Regressive 30/190 (15.8) 18/105 (17.1) Unknown 69/190 (36.3) 32/105(30.5)

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TABLE 3 Summary of Molecular Subtype Characteristics in the DiscoveryCohort. For each molecular subtype, significant associations arereported with each of the 9 gene modules, clinical characteristics,canonical cell type epithelial and white blood cell gene markers, andpathways. PROLIFERATIVE Up-regulated Modules 4, 5, 7 Down-regulatedModules 6 Clinical Characteristics Current smoking ( 

%) Dysplastic biopsies (63%) Biological Charcteristics SCCsubytpes-Classical and Basal; TUB1A1, SCGB1A1 down-regulated: KRT5, KI67up-regulated Pathways Cell cycle: BUB1B/1/3, CHEK2/2, CDK1/2/4/6;E2P1/3/2/4; MCM4/3/5/5/7, TP53, R81 DNA repair: TP53, PARP1, RADS1,BRCA2, FANCA/D2/G/E/M/C, XRCCS/6. ERCC6 Oxidative Phosphorylation andElectron Transport Chain: AtP synthases, NADH-ubiquinoneoxidoreductases, cytochrome C oxidases TFs E2F INFLAMMATORY Up-regulatedModules 1, 2, 7, 8 Down-regulated Modules 6 Clinical CharacteristicsFormer smoking (56%) non-dysplastic biopsies (68%) BiologicalCharcteristics SCC subytpes-Secretory; TUB1A1, MUC5AC down-regulatedPathways Extracellular matrix, focal adhesion, and integrin pathways:colagen, integrin, and laminin genes Cytokine/chemokine:CCL2/14/19/21/28, CXCL12/14/5, CCR1/2/3/4/5, IL1B, IL11RA, IL17RB,IL1R1, IL3RA, EGF, IL15, CK3CR1, TGFB1/B2/B3, KIT Down-regulation ofoxidative phosphorylation, respiratory electron transport, cell cycleTFs SRF SECRETORY Up-regulated Modules 6, 8 Down-regulated Modules 1, 2,5, 7 Clinical Characteristics Current smoking (63%) non-dysplasticbiopsies (66%) Biological Charcteristics SCC subtypes-Secretory: CD45,MUCSAC, TUB1A1 up-regulated; KI67, KRT5 down-regulated PathwaysDown-regulated of extracellular matrix, focal adhesion, integrinpathways TFs Down-regulation of E2F NORMAL Up-regulated Modules 1, 6Down-regulated Modules 8, 9 Clinical Characteristics Former smoking(65%) non-dysplastic biopsies (75%) Biological Charcteristics CD45,MUC5AC, KI67 down-regulated: SCGB1A1, KRT5, TUB1A1 up-regulated PathwaysCore extracellular matrix genes: collagen and lamin genes, WISP1/2Down-regulation of innate and adaptive Immunity: HLA genes, IRF1/4/7/8,TLR2/4/6/8/10, IKBKB TFs Down-regulation of PEA3, IRF, NFKBPROLIFERATIVE Up-regulated Modules 4, 5, 7 Down-regulated Modules 6Clinical Characteristics Current smoking (88%), Dysplastic biopsies(63%) Biological Charcteristics LUSC subytpes-Classical and basal;TUB1A1, SCG81A1 down-regulated; KRT5, KI67 up-regulated Pathways Cellcycle: BUB1B/1/3, CHEX1/2, CDK1/2/4/6, E2F3/3/2/4, MCM4/3/5/6/7, TP53,RB1 DNA repair: TP53, PARP1, RAD51, BRCA2, FANCA/D2/G/E/M/C, XRCC5/6,ERCC6 Oxidative Phosphorylation and Electron Transport Chain: ATPsynthases, NADH-ubiquinone oxidoreductases, cytochrome C oxidasesTranscription Factors E2F INFLAMMATORY Up-regulated Modules 1, 2, 7, 8Down-regulated Modules 4, 5, 6 Clinical Characteristics Former smoking(59%), non-dysplastic biopsies (68%) Biological Charcteristics LUSCsubytpes-Secretory TUB1A1, MUC5AC down-regulated Pathways Extracellularmatrix, focal adhesion, and ntegrin pathways: collagen, itegrin, andlaminin genes Cytokine/chemokine: CCL2/14/19/21/28, CXCL12/14/5,CCR1/2/3/4/5, IL18, IL1IRA, IL17R8, IL1R1, IL3RA, EGF, IL15, CX3CR1,TGF81/82/83, KIT Down-regulation of oxidative phosphorylationrespiratory electron transport, cell cycle Transcription Factors SRFSECRETORY Up-regulated Modules 6, 8 Down-regulated Modules 1, 2, 5, 7Clinical Characteristics Current smoking (77%) non-dyplastic biopsies(66%) Biological Charcteristics LUSC subytpes-Secretory; CD45, MUC5AC,TUB1A1 up-regulated; KI67, KRT5 down-regulated Pathways Down-regulationof extracellular matsix, focal adhesion, integrin pathways TranscriptionFactors Down-regulation of E2F NORMAL-LIKE Up-regulated Modules 1, 6Down-regulated Modules 8, 9 Clinical Characteristics Former smoking(65%) non-dysplastic biopsies (75%) Biological Charcteristics CD45,MUC5AC, KI67 down-regulated; SCGB1A1, KRT5, TUB1A3 up-regulated PathwaysCore Extracellular matrix genes: collagen and laminin genes, WISP1/2Down-regulation of innate and adaptive immunity: HLA genes, IRF1/4/7/8,TLR2/4/6/8/10, IKBK5 Transcription Factors Down-regulation of PEA3, IRF,NFKB

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Example 2: Supplemental Material for Example 1

Materials and Methods

N-nitrosotris-(2-choroethyl)urea (NTCU) mouse sample collection andlibrary preparation. We have previously collected and banked RNA from 40fresh frozen whole lung sections (curls) and laser microdissected (LCM)tissue isolated with an Acrutus Pixcell™ II, from SWR/J and A/J micetreated with NTCU. Mice had been treated topically with 15 or 25 umolNTCU (25 ul of 40 mM NTCU for 15 or 25 weeks) as part of a studyperformed in accordance with IACUC approved protocol at RPCC. Samplesinclude examples of: normal (SWR/J n=3 LCM & 3 curls & A/J n=2 LCM & 1curl), metaplasia/mild dysplasia (SWR/J n=5 LCM & 2 curls), moderatedysplasia (SWR/J n=7 LCM & 4 curls & A/J n=2 LCM & 1 curls), and severedysplasia (SWR/J n=3 LCM & 2 curls), and carcinoma in situ/LUSC (A/J n=2LCM & 2 curls). Samples were extracted using the Qiagen mi-RNAeasy kitaccording to manufacturer's protocol. Sequencing libraries will beprepared from total RNA samples using Illumina® TruSeq® RNA SamplePreparation Kit v2. Each sample was sequenced five per lane on theIllumina® HiSeq 2500 to generate single-end 50-nucleotide reads.

Histological Classification of the NTCU Mouse Samples RNA Sequenced (n =collected/n = passed QC after sequencing) Moderate/ Mouse Sample MildSevere Severe CIS/SCC Stains Type Normal Dysplasia Dysplasia DysplasiaTumor Total A/J LCM 2/2 — 2/2 — 2/1 6/5 A/J Curls 1/1 — 1/1 — 2/1 4/3SWR/J LCM 4/1 5/3 7/3 3/1 19/8  SWR/J Curls 3/3 2/2 4/3 2/1 11/9  Total40/25 Mean RIN values 4.0(1.8) 3.8(0.5) 3.3(0.6) 2.55(0.1) 3.4(1.2) (SD)

NTCU mouse data processing. Demultiplexing and creation of FASTQ fileswere performed using Illumina CASAVA 1.8.2. Trimmomatic was used to trimadapter sequences as well as to trim reads of poor quality using thefollowing parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10, LEADING:20,TRAILING:20, SLIDINGWINDOW:4:20, and MINLEN:20. After trimming, greaterthan 99% of reads were retained in all samples. Samples weresubsequently aligned using mm9 and 2-pass STAR(44) alignment. Gene andtranscript level counts were calculated using RSEM(45) using Ensemblannotation. Quality metrics were calculated by STAR and RSeQC(46).Initially, 15 samples were removed based on percent of uniquely alignedreads (compared to total reads) less than 15%. Subsequent sample andgene filtering was conducted separately on each set as follows: First,EdgeR(48) was used to compute normalized data (library sizes normalizedusing TMM, trimmed mean of M-values, and log 2 counts per millioncomputed) and genes were excluded that either had an interquartile rangeequal to zero or a sum across samples equal or less than 1. Samples wereexcluded based on values greater than 2 standard deviations from themean for 1) mean Pearson correlation with all other samples calculatedacross all filtered genes 2) the 1st or 2nd principal componentscalculated using the filtered gene expression matrix 3) transcriptintegrity number (TIN, computed by RSeQC). After sample filtering, genefiltering was recomputed as described above on the final set ofhigh-quality samples. The data are available from NCBI's Gene ExpressionOmnibus using the accession GSE111091.

Immunofluorescent quantification of cell type and proliferative markers.Basal and ciliated cell type markers (KRT5 and TUB1A1) and theproliferative marker (KI67) were manually enumerated for all epitheliumwithin a biopsy in reference to DAPI staining, with a minimum of 500cells counted per biopsy. The enumeration was conducted on differentregions (independent areas of tissue) present on a slide (1-4regions/biopsy) for each biopsy. A percent of positively stained cellswas calculated for each marker in each region enumerated. A binomialmixed effects model via the 1me4 R package was used to assessdifferences in the percentages of cells staining positive for a givenprotein in each region between the molecular subtypes using the totalcells stained in each region as weights and adjusting for patient as arandom effect.

TCGA SCC tumors data processing. Log 2 transcript per million dataacross 20,500 genes from 476 LUSC tumors was obtained from Campbell (10)et al. Genes were excluded that either had an interquartile range equalto zero or a sum across samples equal or less than 1. Samples wereexcluded based on values greater than 2 standard deviations from themean for more than one of the following criteria: 1) mean Pearsoncorrelation with all other samples calculated across all filtered genes2) the 1st or 2nd principal components calculated using the filteredgene expression matrix 3) transcript integrity number (TIN, computed byRSeQC). After sample filtering, gene filtering was recomputed asdescribed above (n=17,887 genes) on the final set of high-qualitysamples (n=471 tumors).

Table 5 depicts pathways enriched in the Gene Modules. Enrichr results(FDR<0.05) for selected pathways associated with each gene modules.

Biological FDR for Pathways Difference Number Associated between Moduleof with Gene Molecular Number Genes Modules Key Genes Subtypes 1 514Extracellular Matrix/ Collagens, Lamins, 2.70E−36 Cell Adhesion TGFb 2939 mRNA processing RBMs & SRSF 7.20E−05 and splicing 3 20Transcriptional JUN & FOS 1.90E−01 regulation in response tostimuli-(AP-1) Immediate/Early response genes 4 64 OXPHOS/ETC/TCA COXs &NDUFs 3.30E−07 5 209 Cell Cycle/DNA PCNA, TOP2A, 2.00E−31replication/DNA CDC, AURK, repair RAD, XRCC 6 1295 Cilium organizationFOXJ1, DYNC 6.60E−57 and assembly 7 180 Ribosomal Proteins/ RPLs & RPSs1.90E−13 Translation 8 603 Immune Activation CD8A, CD86, 3.30E−07 andInflammatory GATA, STAT, Response IL1B, CD163, (leukocyte/lymphocyteCD68 regulation) 9 112 Interferon signaling SP100, HLAs, 1.30E−02 andAntigen STAT1 Processing and Presentation

TABLE 6 Molecular Subtype associations with Clinical and BiologicalCharacteristics within the Discovery Cohort (DC) and the ValidationCohort (VC). Statistical tests within the Discovery and Validationcohorts were performed using Fisher's Exact Fisher's Exact TestMolecular Subtype V. Variable Variable DC P-value VC P-value GenomicSmoking Status 1.00E−07 9.64E−03 Subject 9.66E−05 5.87E−03 Subject/Time6.96E−04 1.40E−02 Histology 6.75E−03 9.99E−08 Location 2.57E−02 6.69E−01Subject/Location 6.01E−02 1.95E−01 Asbestos Exposure 1.23E−01 7.47E−02Lung Cancer History 1.32E−01 9.92E−01 Progression Status 1.60E−011.67E−05 High-risk Job 4.31E−01 8.30E−01 Sex 5.62E−01 8.90E−01 LUSCTumor Subtype 9.99E−08 1.80E−06 COPD 1.62E−01 9.38E−03 Genomic SmokingStatus 2.71E−09 2.72E−04 Subject 9.66E−05 5.87E−03 Subject/Time 6.96E−041.40E−02 Histology 6.75E−03 9.99E−08 Location 2.57E−02 6.69E−01Subject/Location 6.01E−02 1.95E−01 Asbestos Exposure 1.23E−01 7.47E−02Lung Cancer History 1.32E−01 9.92E−01 Progression Status 1.60E−011.67E−05 High-risk Job 4.31E−01 8.30E−01 Sex 5.62E−01 8.90E−01 LUSCTumor Subtype 9.99E−08 1.80E−06 COPD Status 1.62E−01 9.38E−03

TABLE 7 Statistical associations between Progression/Persistence versusRegression within each Molecular Subtype and Cohort (DC and VC) for eachGene Module. P-values less than 0.05 are reported. ns = not significantand N/A = not enough samples in each group to conduct the analysis. Formolecular subtype, N = normal, S = secretory, I = inflammatory, and P =proflierative Molecular Subtype N N S S I I P P Cohort DC VC DC VC DC VCDC VC Number of Progressive/Persistent Lesions 5 1 17 7 7 5 15 7 ModuleNumber of Regressive Lesions Number 3 3 8 1 4 1 15 13 1 ns N/A ns N/A nsN/A ns ns 2 ns N/A ns N/A ns N/A ns ns 3 ns N/A ns N/A ns N/A 0.047  ns4 0.026 N/A ns N/A ns N/A ns ns 5 ns N/A ns N/A ns N/A ns ns 6 ns N/A nsN/A ns N/A ns ns 7 ns N/A ns N/A ns N/A ns ns 8 0.027 N/A ns N/A 0.005N/A ns ns 9 ns N/A ns N/A ns N/A 0.0017 0.03 1 ns N/A ns N/A ns N/A nsns 2 ns N/A ns N/A ns N/A ns ns 3 ns N/A ns N/A ns N/A 0.047  ns 4 0.026N/A ns N/A ns N/A ns ns 5 ns N/A ns N/A ns N/A ns ns 6 ns N/A ns N/A nsN/A ns ns 7 ns N/A ns N/A ns N/A ns ns 8 0.027 N/A ns N/A 0.005 N/A nsns 9 ns N/A ns N/A ns N/A 0.0017 0.03

TABLE 8 Lung sites where Endobronchial Biopsies were obtained. The sitecode, name, and description are reported for each site. ID NameDescription 096 VC True Vocal Cords, Neck 051 Mouth Floor of Mouth 007EPIG Epiglottis 005 ART Arytenoids 008 FVC False Vocal Cords 095 TRTrachea 050 MC Main Carina, Carina NOS 086 RMB Right Main Bronchus, inclSecondary Carina right 091 RUL Right Upper Lobe 093 RULO Right UpperLobe Orifice or opening 094 RULS Right Upper Lobe Stump 092 RULB RightUpper Lobe Bronchus 087 RML Right Middle Lobe 089 RMLO Right Middle LobeOrifice or opening 090 RMLS Right Middle Lobe Stump 088 RMLB RightMiddle Lobe Bronchus 082 RLL Right Lower Lobe 084 RLLO Right Lower LobeOrifice 085 RLLS Right Lower Lobe Stump 083 RLLB Right Lower LobeBronchus 006 BI Bronchus Intermedius 052 RB1 RUL Apical Segment (AS) 060RB2 RUL Posterior Segment (PS) 063 RB3 RUL Anterior Segment (ANTS) 053RB1/2 RUL Carina between RB1 and RB2 054 RB1/3 RUL Carina between RB1and RB3 061 RB2/3 RUL Carina between RB2 and RB3 059 RB1A/B RUL ASCarina between RB1 A and B 062 RB2A/B RUL PS Carina between RB2 A and B064 RB3A/B RUL ANTS Carina between RB3 A and B 065 RB4 RML LateralSegment (LS) 068 RB5 RML Medial Segment (MS) 066 RB4/5 RML LS Carinabetween RB4 and RB5 067 RB4A/B RML LS Carina between RB4 A and B 069RB5A/B RML MS Carina between RB5 A and B 070 RB6 RLL Superior BasalSegment (SBS) 071 RB6A/B RLL SBS Carina between RB6A and B 072 RB6A/CRLL SBS Carina between RB6A and C 073 RB6B/C RLL SBS Carina between RB6Band C 074 RB7 RLL Medial Basal Segment (MBS) 075 RB7A/B RLL MBS Carinabetween RB7A and B 076 RB8 RLL Anterior Basal Seg (ABS) 077 RB8/9 RLLABS Carina between RB8 and RB9 078 RB8A/B RLL ABS Carina between RB8Aand B 079 RB9 RLL Lateral Basal Segment (LBS) 080 RB9/10 RLL LBS Carinabetween RB9 and RB10 081 RB9A/B RLL LBS Carina between RB9A and B 055RB10 RLL Posterior Basal Segment (PBS) 056 RB10A/B RLL PBS Carinabetween RB10A and B 057 RB10A/C RLL PBS Carina between RB10A and C 058RB10B/C RLL PBS Carina between RB10B and C 001 666 Location wassurgically altered or removed 002 777 Abstractor needs clinician help tocode 003 888 Location code is unknown, illegible 004 999 Location codeis blank, not noted 043 LMB Left Main Bronchus, incl Secondary Carinaleft 044 LMBD Left Main Bronchus, Distal 046 LUL Left Upper Lobe 048LULO Left Upper Lobe Orifice or opening 049 LULS Left Upper Lobe Stump035 LGL Lingula 037 LGLO Lingula Orifice or opening 038 LGLS LingulaStump 047 LULB Left Upper Lobe Bronchus 045 LUDB Left Upper DivisionBronchus 036 LGLDB Lingular Division Bronchus, lingular bronchus 039 LLLLeft Lower Lobe 041 LLLO Left Lower Lobe Orifice or opening 042 LLLSLeft Lower Lobe Stump 040 LLLB Left Lower Lobe Bronchus 009 LB1 + 2 LULApical-Posterior Segment (APS) 018 LB3 LUL Anterior Segment 011 LB1/2LUL APS Carina between LB1 and LB2 010 LB1 + 2/3 LUL APS Carina betweenLB1 + 2 and LB3 016 LB2A/C LUL APS Carina between LB2 A and C 017 LB2B/CLUL APS Carina between LB2B and C 019 LB3A/B LUL ANTS Carina betweenLB3A and B 020 LB4 LUL Superior Lingular Segment (SLS) 023 LB5 LULInferior Lingular Segment (ILS) 021 LB4/5 LUL SLS Carina between LB4 andLB5 022 LB4A/B LUL SLS Carina between LB4A and B 024 LB5A/B LUL ILSCarina between LB5A and B 025 LB6 LLL Superior Segment (SS) 026 LB6A/BLLL SS Carina between LB6A and B 027 LB6A/C LLL SS Carina between LB6Aand C 028 LB6B/C LLL SS Carina between LB6B and C 029 LB8 LLL AnteroMedial Basal Segment (AMBS) 030 LB8/9 LLL AMBS Carina between LB8 andLB9 031 LB8A/B LLL AMBS Carina between LB8A and B 032 LB9 LLL LateralBasal Segment (LBS) 033 LB9/10 LLL LBS Carina between LB9 and LB 10 034LB9A/B LLL LBS Carina between LB9A and B 012 LB10 LLL Posterior BasalSegment (PBS) 013 LB10A/B LLL PBS Carina between LB10A and B 014 LB10A/CLLL PBS Carina between LB10A and C 015 LB10B/C LLL PBS Carina betweenLB10B and C

TABLE 9 Antibodies used in the Immunofluorescence Studies. AntigenAntibody Company Catalog Dilution retrival Species Immune cell typemarkers CD68 Dako m0876 1- AR6 mous CD163 Cell Marque 163m-16 1-100 AR9mous CD4 Thermo Fisher ms1528S 1-100 AR9 mous CD8 Dako M7103 1-100 AR9mous Epithelial cell type and proliferation markers Ac-α-Tub Sigma T67931-100 citrat mous KRT5 BioLegend 905-901 1-100 citrat chicken KI67 Abeamab16667 1-100 citrat rabbit

TABLE 10 Genomic smoking status over time by subject. The smoking statusof each subject at each time point was computed based on a previouslypublished smoking-associated gene signature⁶ (see methods for details).The rows indicate the smoking status across all time points sampled foreach patient. The −> symbol indicates changes in smoking status overtime. There is not a statistical difference between the distribution ofsubjects in the smoking status categories between the discovery andvalidation cohorts by a two-sided Fisher's exact Test (p = 0.90). Sourcedata are provided as a Source Data file. Discovery Cohort ValidationCohort Genomic smoking status over time Number of Subjects Number ofSubjects Current 9 9 Former 10 5 Current->Former 7 4 F ormer->Current 32 Current->Former->Current 1 0

TABLE 12 Molecular Subtype associations with previous history of lungcancer. Previous history of lung cancer (LC) was categorized as follows:no history (No LC History), a previous history of LC that include a lungsquamous cell carcinoma (LC History - LUSC), and a previous history ofLC that does not include a lung squamous cell carcinoma (LC History -Other). Statistical tests within the discovery and validation cohortswere performed using two-sided Fisher's exact tests. Discovery CohortBiopsies (n = 190) Validation Cohort Biopsies (n = 105) No LC LCHistory - LC History - No LC LC History - LC History - Variable HistoryLUSC Other P-Value History LUSC Other P-Value Molecular SubtypeProliferative 14 5 33 12 9 7 Inflammatory 10 6 21 12 4 14 Secretory 26 827 14 13 7 Normal-like 9 3 28 p = 0.19 6 1 6 p = 0.10

What is claimed herein is:
 1. A method comprising measuring the level ofexpression of at least one module 9 gene in a sample obtained from asubject, wherein the at least one module 9 gene is selected from thegroup consisting of: LAP3; NUB1; CD74; BTN3A1; EIF2AK2; PARP12; SP100;IFI35; LAG3; PSME1; APOL4; APOL1; PSME2; TRIM14; DDX58; OAS3; OAS2;BTN3A3; BTN2A1; XRN1; IFIH1; STAT1; GBP1; IFIT3; TNFSF10; OPTN; NMI;ZNFX1; RNF114; BTN2A2; IRF1; IFI6; APOL3; APOL2; BST2; KLHDC7B; HELZ2;IDO1; TRIM21; TRIM22; EPSTI1; CMPK2; TRAFD1; TOR1B; DDX60; IFI44L;IFI44; PARP9; HERC6; CXCL9; WARS; PML; NLRC5; IFIT5; UBE2L6; MX1; USF1;ADAR; LY6E; GBP4; DTX3L; IL15; IFI27; C2; B2M; BATF2; TAP1; LGALS9;CXCL10; PARP14; RNF213; SAMD9L; HLA-DQB1; CIITA; SOCS1; SP140L; TRIM69;BTN3A2; ISG15; RUFY4; PLSCR1; HLA-DRB1; HLA-DQA1; ACSL5; C5orf56;HLA-DOA; HLA-DMA; TAPSAR1; PSMB8; HLA-DRA; HLA-C; HLA-E; HLA-F; PSMB10;EXOC3L4; HCP5; HLA-A; UBD; IRF9; APOL6; HLA-DPB1; PSME2P2; GBP1P1;HLA-DPA1; TAPBP; HLA-DQB2; HLA-B; OR2I1P; PSMB9; and HLA-DMB.
 2. Themethod of claim 1, wherein the at least one module 9 gene is selectedfrom the group consisting of: CIITA; NLRC5; EPSTI1; UBE2L6; B2M andTAP1.
 3. The method of claim 1, wherein the at least one module 9 geneis selected from the group consisting of: CIITA; NLRC5; and EPSTI1. 4.The method of claim 1, further comprising measuring the level ofexpression of at least one module 10 gene in the sample, wherein the atleast one module 10 gene is selected from the group consisting of:CACNB3 and MAPK10.
 5. The method of claim 1, wherein the samplecomprises morphologically-normal tissues or morphologically-normalcells.
 6. The method of claim 5, further comprising bronchialpremalignant lesion cells.
 7. The method of claim 1, wherein the sampleconsists of morphologically-normal tissues or morphologically-normalcells.
 8. The method of claim 1, wherein the sample comprises abronchial brushing obtained from the right or left mainstem bronchus, anendobronchial biopsy, an endobronchial brushing sample, a large airwaybiopsy, a large airway brushing sample, a nasal epithelial cell, orsputum.
 9. The method of claim 1, wherein the subject is subject havingbronchial premalignant lesions.
 10. The method of claim 1, wherein thesubject is presently lung cancer-free.
 11. The method of claim 1,wherein the subject is a smoker or former smoker.
 12. The method ofclaim 1, wherein the subject is one who does not presently have and hasnot previously had lung cancer.
 13. The method of claim 1, wherein thelevel of expression of no more than 1,000 genes is determined.
 14. Themethod of claim 1, wherein the level of expression of no more than 200other genes is determined.
 15. The method of claim 1, further comprisingadministering to the subject a chest CT scan.
 16. The method of claim 1,further comprising administering to the subject a bronchoscopy-basedprocedure.
 17. The method of claim 1, further comprising administeringto the subject at least one anti-proliferative drug or at least oneimmune stimulating drug.
 18. The method of claim 1, further comprisingmeasuring the level of expression of at least one module 5 gene, whereinthe at least one module 5 gene is selected from the group consisting of:RACGAP1; TPX2; C1orf112; POLDIP2; DBF4; E2F2; NCAPD2; ANLN; DEPDC1;UHRF1; SPDL1; TSPAN17; RFC2; RAD51; NOP58; ASPM; PRR11; HMMR; GTSE1;WDR62; UBE2T; NDC80; ORC1; RAD54L; PIGS; AURKA; BIRCS; KIF4A; ORC6;CDC45; CDC6; CDC7; MCM5; CDKN3; LGMN; GINS1; MYBL2; E2F1; SUV39H1;CENPI; GABPB1; MCM4; RNASEH2A; ASF1B; ILVBL; EZH2; UBE2S; NCAPG; FOXM1;RAD51AP1; RFCS; TIMELESS; MCM3; BYSL; TTK; KIF20A; LMNB1; SMC4; LRRC42;HDAC1; TTF2; CDC20; STMN1; CENPF; KIF14; HELLS; MTHFD1L; MASTL; CCDC77;TMPO; NCAPH; KIF18A; CCDC18; HNRNPA2B1; ZWINT; CENPK; TUBA1B; HJURP;CKS2; CSE1L; SOX4; C17orf53; HNRNPR; DLGAP5; PKMYT1; A4GALT; KNSTRN;FAM64A; PVRL2; GINS2; ABCB7; TOP2A; MRPL35; PCNA; CCNB1; CDCA8; TROAP;ESPL1; URB2; STX6; CKAP2; BORA; BRIP1; CTSV; CPEB2; NUSAP1; KIF23;CASC5; CENPO; KIF11; CEP55; WDR12; CENPE; BRCA2; DENR; DIAPH3; FANCI;PLK4; KIF2C; NUF2; DTL; INTS7; ILF2; CHAC2; FANCD2; CCNA2; SKP2; G3BP1;MTFR2; CDCA5; NCAPG2; NONO; RBMX; GINS4; MKI67; CHEK1; TEX30; CENPH;SKA1; EME1; BUB1B; CCNB2; CHAF1B; SPC24; C16orf59; CCNF; KIAA1524;KIF15; RPL39L; SLBP; CDC25A; MAD2L1; PTTG1; MELK; SKA3; CENPN; KIAA0101;PLK1; CDT1; TK1; PBK; DTYMK; RFWD3; FEN1; USP39; CKAP2L; BUB1; CDK1;SHCBP1; ESCO2; RRM2; CKS1B; ZWILCH; UBE2C; CKAP5; CCNE2; TYMS; B3GNT8;AURKB; RCC2; FARSA; MAF1; KPNA2; SKA2; TRAIP; LIN9; IQGAP3; CDCA2;PARPBP; KIF18B; ERCC6L; PTMA; FANCA; H2AFX; FAM72B; FAM111B; XRCC6;FAM72A; XRCC2; HYLS1; ARHGAP11A; PRC1; CENPW; LSM2; TRIM59; FAM72D;DHFR; KIFC1; and PGAM5.
 19. The method of claim 1, further comprisingmeasuring the level of expression of at least one module 6 gene, whereinthe at least one module 6 gene is selected from the group consisting of:NEK11; IFT88; STPG1; KLHL13; SLC7A2; ZMYND10; ARX; DHX33; WDR54;ARHGAP44; CDKL3; PROM1; DNAH9; GAS7; RHBDF1; TEAD3; JARID2; FUZ; LRRC23;MKS1; TTC19; PPP5C; IL20RA; GLT8D1; PLEKHB1; NRXN3; CCDC28A; HSF2;TOMM34; CD44; EFCAB1; USP2; NSUN2; DNAH5; SPATA7; TRIT1; CC2D2A; SNX29;R3HDM1; SRD5A2; NEDD4L; PPP1R3F; ARHGEF5; POLQ; LY75; SDCCAG8; HHAT;GALC; GYG2; DCBLD2; LAMC2; SPA17; SNCAIP; ANKS1A; DGKA; TBC1D22B; FOXJ2;DIP2B; ZMYND12; NGEF; EML1; EVI5; TP53BP1; ATP11A; IFT80; PPP2R5B; MNT;AP3M2; ST6GALNAC2; C16orf80; TRIP13; RPS6KA6; RHOBTB1; XRCC1; CLCN4;SLC24A1; ARHGEF10L; SRI; GRAMD4; TMEM131; KIFAP3; SPAG6; POLD3; FKBP6;TULP3; ZCWPW1; TP73; OSBPL6; CDC14A; RFX3; PIH1D3; HSP90AA1; HSPB11;ULK2; MAPRE3; CD59; WDR47; NFX1; IPO11; MTMR2; ATXN7L3; SF3B2; TFAP2C;RFX2; GP6; REM1; KIF9; NSFL1C; PLK1S1; DYNLL1; SLC8B1; DZANK1; C20orf26;TASP1; NUDC; CERS4; NAT14; IL5RA; TEKT2; PSMD5; NUP188; ITPR3; IFT74;SEC14L3; ANKRD54; CENPM; CBY1; RTDR1; RAB36; TTLL1; MCAT; MYH9; DESI1;CERK; KHNYN; PRMT5; CDKL1; SAMD15; AHSA1; SIX4; RPS6KA5; IFT52; SPEF1;EPPIN; MOSPD1; ASB9; PCYT1B; KLF8; FGF14; CDADC1; MRPS31; SLC25A15;KATNAL1; GDPD3; MMP15; CCDC113; SLC38A7; HSDL1; NAGPA; USP10; METRN;CLUAP1; RPGRIP1L; CCP110; IQCH; CORO2B; ACSBG1; ZNF106; CEP152; RP1;NIPAL2; ZC2HC1A; CHRAC1; NCALD; SQLE; TUSC3; POLR2I; ZFR2; CAPS; TTC26;RNF32; IQCE; HIBADH; TAX1BP1; FAM188B; RPA3; NRF1; CEP41; FSD1L; AK1;RGP1; MPDZ; GLIS3; HPS1; LZTS2; SH3PXD2A; PBLD; TRIM37; DHX40; GALK1;B9D1; PEX12; HNF1B; PPP1R9B; PRKAR1A; EFNB3; IFT20; SLAIN2; WFS1;TBC1D19; WHSC1; SNX25; LRP2BP; C11orf63; SNX15; KIAA1377; PPFIBP1; ELK3;PRMT8; AKAP3; KCNA1; LTBR; OGFOD2; STX2; MDM1; UHRF1BP1L; ENO2; ST8SIA1;RSPH4A; MAK; MCM9; FAM184A; TPD52L1; SASH1; RBM24; CAP2; PACRG;C6orf118; MDFI; FAM120B; DNPH1; ENPP5; NME5; IK; MSH3; RAD1; C5orf15;WWC1; CLDN16; ARL6; IFT57; HHLA2; IQCG; KIAA1257; PLCH1; NEK4; STEAP3;STAM2; NRBP1; DNAH6; PECR; GGCX; PPP1R7; TAF1B; ORC4; THADA; C2orf42;GRIN3B; ALMS1; BCL9; TRIM62; DNAJC6; PHTF1; OSCP1; TBCE; RIMS3; CCDC181;RCAN3; IFT46; CASC1; FILIP1; HMGN3; UBE3D; ARMC2; WDR35; DNAH7; C2orf40;FAM206A; WDR34; CNTRL; TRIM32; FBXW2; CCDC176; ACYP1; IFT43; DNAL1;TTLL5; DLST; PPP4R4; ZC2HC1C; FKBP1B; CCDC147; C10orf95; LRP11; CCDC170;MYCT1; CYSTM1; ENOX1; PROSER1; HSPH1; AKAP1; ZSCAN18; TRMT1L; CRY2;FAM35A; BBS9; IFT81; TTC21B; B9D2; DAW1; ENKD1; C20orf85; TCP11;COL21A1; BBS2; PTGER2; TEKT3; TTF1; C20orf195; TRIP10; PANK2; MGME1;ID1; ERGIC3; HECTD3; FRMD8; PRDX5; PCNXL4; KTN1; SIX1; WDR60; LRRC61;TUBA4A; TNFRSF19; AKAP9; STYXL1; C22orf23; RIBC2; CDHR3; RABL5; KLHDC10;TTBK2; C15orf57; CALML4; THAP10; BBOX1; LRRC6; EGLN3; FOXJ1; CDC16;RSPH3; STK33; CACNG6; SSBP4; UBAC1; TUBGCP2; ARHGEF16; ATPIF1; PRRG1;KIF3A; PSMC3IP; NPHP4; MAP1B; PDHA1; ZSCAN5A; RHPN2; ABHD12B; ZSWIM4;FBXW9; ZNF20; SPATA6; GAS2L2; CNGA4; IQCA1; VPS13B; RGS22; BTBD3;POLR3F; DPH2; PIK3C2B; SLC41A1; SPG20; STOML3; MORC4; EPHB2; PDE6B;SEC14L4; ACTR3B; LRRIQ1; TMEM254; LRRCC1; UNC79; MEIS2; PTGFRN; ISCA1;CCDC146; HILPDA; KIAA1009; LCA5; PRPH; KCNH3; CD164; LACE1; PKIB; REPS1;ARMC9; TSGA10; TGFBRAP1; APPL2; TTC5; NMT1; MYCBPAP; VEZF1; SAP130;ODF2; WDR38; SLC22A23; BPHL; FAM8A1; C6orf52; TTC29; ANKRD42; NEK1;C11orf70; BTG4; PAQR5; LRRC49; GIPC2; IFT172; DYNC2L11; SMEK2; ARL3;MDH1B; CIR1; ABI2; MNS1; HCN4; FAM13A; RASGEF1B; CDKL2; SHROOM3; MTTP;CCDC65; CERS5; MORN3; C14orf37; SLC38A6; EFCAB11; PTGR2; AK7; SLC27A2;DNAJA4; BBS4; CCDC33; WDR93; FURIN; SH3GL3; GLYR1; NUDT7; GALNS; GASB;GFOD2; LRRC46; BCAS3; WRAP53; TP53; WDR45B; FBX015; FHAD1; PEX14;IL22RA1; STRIP1; NME7; UCK2; UFC1; USP21; DYRK3; SMYD2; ADAM15; AQP10;C1orf131; SCCPDH; CNIH3; CALM2; WDPCP; NPHP1; AMMECR1L; SPAG16; ANKMY1;CCDC39; TRMT10A; NAF1; ROPN1L; FAM50B; FARS2; DCDC2; RNF44; TCTE1;CYP39A1; TPBG; IRAK1BP1; ARHGAP18; GBAS; PSPH; AGBL3; TMEM27; ZNF157;DIAPH2; PRPS1; CXorf57; MCPH1; CETN2; CHMP7; C9orf72; IDNK; ASTN2;WDR31; CAMK2G; LRRC27; CNNM2; ZNF214; C11orf49; CCDC81; TTC12; C11orf52;GLB1L2; MTA2; MPZL2; PLCB3; CTF1; TMEM218; N6AMT2; SPATA4; FSIP1;DIXDC1; PIH1D2; C2orf50; ENKUR; DCP1B; AKAP6; MIPOL1; NUBPL; VIPAS39;TEX9; INPP1; CCDC122; NBAS; CCDC74B; RPP38; TRIM36; SPEF2; CAPSL; WDR78;IFLTD1; CLGN; CETN3; CCDC148; FAM81B; ADPRHL1; FBXL2; UBP1; LURAP1L;CFDP1; FAM92B; FBXO36; ZNF599; DDAH1; ANKFN1; FAM105B; FAM134B; CEP112;ENAH; CCDC173; SORBS2; SLFN13; RAB6B; ACSS1; RSPH10B; AK9; AZIN1;AGPAT5; LRGUK; KDM8; ALS2CR12; SPAG17; FMN2; GRIP1; ELMSAN1; GNA14;FAM161B; DRAM2; C8orf37; C15orf26; WHAMM; TIAM1; RPGR; SH3RF2; GALK2;MMP14; C1orf158; HYDIN; ZNF19; FAM81A; DSCR3; LCA5L; C9orf43; WDR19;DRC1; RAB28; WDR66; LRRC43; AAED1; FAIM; SLC13A3; RIBC1; C2orf62; KCNB1;DNAH3; AGPAT6; B4GALT3; C21orf59; C2orf81; CHCHD6; TPPP3; ZDHHC1; IQCC;KALRN; TMPRSS3; RSPH1; C9orf116; PCSK7; RUSC1; UBQLN4; TONSL; ORAI2;LRWD1; FBXL13; DUSP14; LRRC56; FDXR; ALOX15; HS3ST6; SHANK2; PPP1R32;RPS6KA4; UBXN10; C1orf87; OMA1; DNAJB4; LRRIQ3; WDR63; KLHDC9; FLVCR1;SPATA17; DUSP19; CCDC104; CCDC138; CCDC74A; TEKT4; SPATA18; INHBB; BBS5;RPRD2; PACRGL; DHX57; FZD5; C1orf189; FAM175A; HIPK1; NEK10; AZI2;GLB1L; EFHB; ICA1L; KIAA1407; CDS1; GMPS; ABHD6; LZTFL1; MEAF6; DNALI1;EXO5; PRSS12; MAPS; CEP44; ZNF474; PRIMPOL; GDF9; GJB7; TXLNB; DCBLD1;KIAA0895; KIF6; SYTL3; IQUB; C7orf57; MED30; HEATR2; TP531NP1; TMEM67;FAM219A; C9orf24; ABCA1; C8orf34; KDM1B; C9orf64; SVEP1; CXorf22;KIAA1958; STRBP; GAPVD1; ARMC3; LRRC18; DNAAF2; TTC8; AK8; C9orf9;ZMYND19; STOX1; PPP1R36; CKB; DPCD; LARP6; C16orf71; FAM227B; STXBP4;C10orf32; SMPD1; APBB1; C11orf65; C11orf74; TUB; XRRA1; C16orf46; ZNF3;IQCD; RRAD; WDR16; CCNDBP1; MS4A8; MAP1A; DUSP18; TTC16; COQ4; CCDC103;ENDOG; COQ7; KATNAL2; SPATA33; RHEBL1; TUBA1A; DNAAF3; HSD11B1L; CYB5D2;TEKT1; TMEM68; ZNF598; C2CD3; ULK4; MOBP; DEGS2; BMP1; SLC20A2; DYNLRB2;VWA3B; LDLRAD4; PKIG; FAM178B; CXXC4; TCTN2; TNIP2; PPIC; ZBBX; ARMC4;NSMCE1; RAB3B; ARL13B; MUC15; TPST1; TOR1AIP2; FABP6; FAM161A;C14orf142; SPATA24; SLC23A1; HSD17B13; KIAA0232; DCDC1; PRKCE; MORN4;RBKS; NAT1; LPAR3; MAP6; ZNF584; DNAI2; LRRC34; CTPS1; KNDC1; AQP4;LRRC48; SNTB1; COPRS; CCDC11; RSPH9; KLHL6; ZFAND4; ADH6; CCDC96; ABCD2;IQCB1; APOBEC4; PIFO; CEP19; FAM174A; GSTA3; CHRNA9; C12orf76; BBS1;ZNF497; IQCK; SH3PXD2B; WDR49; THAP6; BTC; CATSPERD; APITD1; EIF1AD;TEX26; GPR156; RUVBL1; UNC119B; TMPRSS7; BNIP3; SMIM19; PRR18; EID2B;PLA2G16; CNTD1; MAP3K19; CCDC121; SEC24C; DSCAML1; MRVI1-AS1; UMODL1;C8orf47; IRX3; CASC2; AGTRAP; C2orf73; MLF1; GRAMD1C; PPP1R42; DALRD3;NT5DC1; MCMDC2; P4HTM; ERBB4; ZNF713; GPS; RIIAD1; C1orf173; TMEM107;CCDC89; C10orf67; ZNF664; PLD6; FAM216B; C1orf194; TRNAU1AP; FGD6;TIGD2; GLIPR1L2; KCNE1; WDFY3-AS2; ZFP3; OXTR; BBS12; NME9; RNF135;GPR135; WRB; CYB5D1; CEP97; FAM104B; NGRN; SPATA13; CSMD1; FANCF;RUVBL2; CCDC60; CDC125; C10orf107; TNFAIP8L3; DGCR6; C11orf88; EFHC2;C9orf66; BTBD9; ANKRD45; DNAH2; HIST2H4A; LRTOMT; EFNA5; C21orf128;PROS1; NELL2; FAM110C; PIGW; RBM43; ZFP90; TMEM121; EFCAB10; LRRC37B;PGBD2; WBP5; PPIL6; KIAA0825; CDNF; ARL15; TNFAIP8L1; RAD51D; SMYD3;MRPL40; MORN5; THNSL1; RASA3; AGBL4; CYP2R1; C2orf76; SLC51B; KLHL32;PRELID2; TMEM212; ANKRD37; AKAP14; ZNF396; FAM86B1; KATNA1; KIF24;LYRM7; TMEM17; TMEM232; FAM183A; EFCAB6; TEAD1; SLIT1; TSPYL4; DYNC2H1;WDR86; IFT140; C17orf97; C1orf170; DNAJB13; AMY1C; MORN2; NWD1; TUBB4B;ENO4; FOCAD; TCTEX1D4; CERKL; C9orf171; C12orf55; FAM154B; SNTN;PTPLAD2; C1orf192; FAM47E; PTPRT; KIF19; TUBB; XPNPEP3; GRM7; ZNF569;C20orf96; ESRRG; MYO18A; TTC30B; ZNF33B; AMZ2; MVB12B; KIAA1211L;HIST3H2BB; DTHD1; SRC; NEK5; SLC22A4; BCO2; KCNMB2; C5orf42; DNAH10;WDR96; C4orf22; MEIG1; LEKR1; CCDC151; NUP62CL; MB; HMGN5; ZNF607;ZNF627; KCNRG; CCDC69; CALM1; FAM179B; PPP1R14C; FOXJ3; INPP5F; TSEN15;CIPC; DZIP3; L3MBTL3; DMD; ARMCX6; INF2; FAM83H-AS1; EFCAB2; TATDN3;ECT2L; FAM229B; DDO; ATP1A1OS; EFCAB7; LDLRAD1; LRRC73; SYS1; TRAF3IP1;NELFE; HSPA1L; LY6G5C; GPANK1; C10orf115; TRIM39; CASC10; C9orf135;TTC25; TCTN1; FAM201A; LRRC10B; TMEM231; C4orf47; TTLL10-AS1; OR7E36P;DENND6B; ITPRIPL2; CRYZL1; PPAPDC2; C21orf49; HN1L; ANKUB1; CCDC19;TCTEX1D2; ZNF625-ZNF20; TMEM110; CENPBD1P1; LIPE-AS1; CLDN9; MYCBP;AMZ2P1; BBIP1; FAM187A; CPEB1; IFRD2; FAM166B; C5orf49; SIAH3; TSTD1;FAM228B; C6orf226; AP4M1; TIAF1; DCDC2B; ZNF844; DNAJC27-AS1;SLC25A5-AS1; LAMTOR5-AS1; PPP1R26-AS1; BAIAP2-AS1; FAM66C; LINC01132;DNMBP-AS1; LINC00948; SRGAP3-AS2; UBAC2-AS1; VIM-AS1; TOB1-AS1; ANKRD66;STMND1; LINC00326; LINC00271; TSPAN19; LYRM9; NKAPP1; PINLYP;SDCBP2-AS1; TEX21P; LINC00094; C12orf75; TOPORS-AS1; SMKR1; LINC00886;HOGA1; SOX2-OT; ZNF709; ARHGEF26-AS1; ZNF487; WDR92; LINC00883; WDR65;WDR86-AS1; TUBA4B; LIFR-AS1; USP2-AS1; BDNF-AS; CRNDE; H2AFJ; ZBED5-AS1;USP51; DYNLL1-AS1; SRP14-AS1; CCDC153; FMN1; UGDH-AS1; SPATS1;LINC01018; LRRC37BP1; GPR162; APITD1-CORT; FAM86EP; STAU2-AS1; ATXN7L3B;RHPN1-AS1; ABCC6P2; DYX1C1; C21orf119; LINC01171; NHLRC4; OR7E47P;LINC00638; AQP4-AS1; C15orf65; LINC00908; MAFG-AS1; ILF3-AS1; C19orf82;RNF157-AS1; NAPA-AS1; HMGN3-AS1; FGF14-AS2; and CASC15.
 20. The methodof claim 1, further comprising measuring the level of expression of atleast one module 7 gene, wherein the at least one module 7 gene isselected from the group consisting of: RPS20; EIF4B; RPL18; RPL31; RPS5;STARD7; RPL6; RPLP0; IGBP1; EIF3L; RPL3; EIF3D; CCNB1IP1; EIF3E; EEF1D;RPS16; FBL; RPS19; GLTSCR2; RPL18A; DDX50; RPL28; RPL19; SMARCD2; RPL34;RPS13; C12orf57; RPS12; RPL24; EEF1B2; RPS15; RPL22; DPH5; RPS25; CCNI;RPL21; RPL5; RPS10; RPL23; SNRPD2; UROD; SERGEF; ECSIT; RPL36; MRPL34;COX4I1; RPL27; TPT1; RPS15A; ATP5G2; RNASEH2B; CCDC115; RPL35; POLR1E;RPS6; RPLP1; RPL7P9; RPS24; RPL14P1; GCSH; RPS2; RPS11; RPL13A; RPL11;RPS8; RPS27A; RPL32; SLC25A26; RPS3A; RPL37; BTF3; RPL10; RPL7; EBAG9;EIF3H; RPL7A; RPS3; FAU; TMEM18; RPL30; EEF1A1; ZNF689; RPL8; RPL26;RPL29; PMVK; RPL9; RPS14; RPL27A; MRPL16; RPL13; RPSA; SLC25A6; CNBP;RPS9; RPS21; RPS7; RPL38; TOMM20; RPL4; MRPL11; RPL15; FAM211A-AS1;EIF3F; ZFAS1; RPLP2; RPS27; RPS17L; RPL35A; RPS7P1; RPS17; RPS23;COMMD6; RPL14; RPS2P46; EEF1A1P5; NACA; TOMM7; RPL37A; RPL12; RPS4X;RPL23A; ZNF511; RPL10A; RPL39; C6orf48; GNB2L1; RPSAP58; RPL15P3;RPL18AP3; RPLP0P6; RPS29; RPL21P75; SMIM7; LYRM4; RPS3AP26; RPL7P1;PHB2; RPL21P28; UBA52; RPL41P1; RPL41; RPL4P4; RPS23P8; RPS18; EEF1B2P3;RPL3P4; EEF1A1P6; RPS28; GAS5; RPS3AP6; RPL24P2; RPL6P27; RPL13AP5;RPS2P5; RPL36A; RPL7AP6; SNHG6; EEF1G; RPL17; and SNHG8.
 21. The methodof claim 1, further comprising measuring the level of expression of atleast one module 4 gene, wherein the at least one module 4 gene isselected from the group consisting of: MRPS24; NDUFB4; NDUFB2; PSMD8;NDUFB7; TOMM22; TCEB2; CHCHD2; PSMD9; MRPL51; COX6A1; COX7A2; ATP5F1;NDUFB3; PDZD11; NDUFA1; MRPS7; ROMO1; COX6B1; TIMM17B; UQCR11; EMC6;COX7B; BLOC1S1; COX5B; PSMB7; NDUFB10; ANAPC11; TXNL4A; SNRPG; NDUFS6;TIMM8B; NDUFC2; DBI; C14orf2; THOC7; UQCRQ; COX6C; NDUFB6; STOML2;NDUFB8; ATP5I; UQCRFS1; MRPL36; MYEOV2; CHCHD1; MINOS1; USMG5; COX8A;POLR2L; TMEM11; COX5A; MRPL54; UQCR10; NDUFA12; DRG1; NDUFA13; SUMO2;NDUFA4; GPN1; C11orf83; NDUFS3; ATP5J2; and MRPL12.